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Elkhorn Slough National Estuarine Research Reserve

Final Management Plan 2007-2011

September 29, 2006


Page No.

Chapter I


A. Purpose & Scope of Management Plan 23

B. Description, Mission, and Goals of the NERRS 24

C. Description & Mission of the Elkhorn Slough NERR 29

D. Description & Mission of CDFG 32

E. Description & Mission of the ESF 32

F. National Focus on Estuarine Conservation 33

G. Conservation of Elkhorn Slough 34

H. References 36

Chapter II


A. Conservation Assessment Framework 39

B. Description of Watershed Conservation Threats 42

C. ESNERR Conservation & Organizational Goals 43

D. Prioritization of Goals & Actions 47

E. Strategic Planning & Adaptive Management 47

F. References 48

Chapter III



A. Introduction 50

B. Objectives & Strategies 57

C. References 61

Chapter IV



A. Introduction 63

B. Objectives & Strategies 67

C. References 71

Chapter V



A. Introduction 73

B. Objectives & Strategies 78

C. References 82

Chapter VI



A. Introduction 84

B. Objectives & Strategies 89

C. References 91

Chapter VII



A. Introduction 95

B. Objectives & Strategies 98

C. References 100

Chapter VIII



A. Introduction 102

B. Objectives & Strategies 104

C. References 106

Chapter IX




A. Introduction 108

B. Objectives & Strategies 112

C. References 113

D. Monitoring Table 114

Chapter X





A. Introduction 116

B. Objectives & Strategies 118

C. References 122
Chapter XI



A. Introduction 123

B. Objectives & Strategies 123

Chapter XII


A. Introduction 133

B. Visitor’s Center 133

C. Reserve Trails 135

D. Reserve Regulations & Enforcement 137

E. ADA Accessibility of Reserve 137

F. Public Access Near the Reserve 138

G. Objectives & Strategies 139
Chapter XIII


A. Introduction 141

B. Priorities 143

C. Strategies 143
Chapter XIV


A. Need for Administration Program 145

B. Program History 145

C. Program Purpose & Goals 145

D. Program Description 146

E. Program Staffing & Working Groups 153

F. Guiding Documents & References 153

Chapter XV


A. Need for Volunteer Program 155

B. Program History 155

C. Program Purpose & Goals 156

D. Program Description 157

E. Program Staffing & Working Groups 162

F. Guiding Documents & References 162

Chapter XVI


A. NERR Education Plan 163

B. Need for Education Program 165

C. Program History 167

D. Program Purpose & Goals 169

E. Program Description 172

F. Program Staffing & Working Groups 178

G. Guiding Documents & References 180
Chapter XVII


A. NERR Research Plan 181

B. Need for Research Program 184

C. Program History 185

D. Program Purpose & Goals 186

E. Program Description 187

F. Program Staffing & Working Groups 193

G. Guiding Documents & References 194
Chapter XVIII


A. Need for Stewardship Program 195

B. Program History 196

C. Program Purpose & Goals 196

D. Program Description 197

E. Program Staffing & Working Groups 201

F. Guiding Documents & References 202

Chapter IXX


A. Need for Operations & Facilities Program 203

B. Program History 203

C. Program Purpose & Goals 204

D. Program Description 204

E. Program Staffing & Working Groups 206

F. Guiding Documents & References 207




The preparation of this document was funded by the California Wildlife Conservation Board and made possible through the cooperative efforts of the staff of the Elkhorn Slough National Estuarine Research Reserve, the National Oceanic and Atmospheric Administration’s Estuarine Reserves Division, and the California Department of Fish and Game. This plan was greatly strengthened by the technical expertise and insight of the following external reviewers:

  • The Elkhorn Slough Foundation

  • The Elkhorn Slough National Estuarine Research Reserve Advisory Committee

  • The Elkhorn Slough National Estuarine Research Reserve Volunteers

  • Teresa LeBlanc, California Department of Fish and Game

  • Betsy Bolster, California Department of Fish and Game

  • Diana Hickson, California Department of Fish and Game

  • Carl Wilcox, California Department of Fish and Game

  • Eric Larson, California Department of Fish and Game

  • Pati Delgado, National Oceanic and Atmospheric Administration

  • Erica Seiden, National Oceanic and Atmospheric Administration

  • Craig Cornu, South Slough National Estuarine Research Reserve

  • Jeff Crooks, Tijuana River National Estuarine Research Reserve

  • Ted Grosholz, University of California, Davis

  • Steve Lonhart, Monterey Bay National Marine Sanctuary

  • Drew Talley, San Francisco National Estuarine Research Reserve

  • Brian Anderson, Granite Canyon Marine Laboratory & University of California, Davis

  • Ken Johnson, Monterey Bay Aquarium Research Institute

  • Bryan Largay, Resource Conservation District of Monterey County

  • Marc Los Huertos, University of California, Santa Cruz

  • Susan J. Frankel, USDA-Forest Service, Pacific Southwest Research Station

  • Jeff Kwasny, Los Padres National Forest

  • Douglas D. McCreary, Sierra Foothill Research and Extension Center

  • Sarah Davies, San Francisco Bay National Estuarine Research Reserve

  • Tom Gaskill, South Slough National Estuarine Research Reserve

  • Dawn Hayes, Monterey Bay National Marine Sanctuary

  • Thomas Christensen, Monterey Peninsula Water Management District

  • Gage Dayton, Moss Landing Marine Laboratory

Executive Summary

This document is the second edition of the management plan for the Elkhorn Slough National Estuarine Research Reserve (Elkhorn Sough NERR), and covers the period from 2007-2011. The plan provides an update to the Elkhorn Slough National Estuarine Research Reserve Management Plan, 1985—the first management plan developed for the Reserve.

The Elkhorn Slough NERR is an ecologically diverse 583 hectare (1,439 acre) protected area located on the eastern shore of the Elkhorn Slough, near the Monterey Bay in Central California. Elkhorn Slough is a seven-mile arm of the Monterey Bay located half way between the cities of Santa Cruz and Monterey. This arm bends as it extends inland, and at the “elbow” lies the Reserve.
The Elkhorn Slough NERR is protected for long-term research, water-quality monitoring, education and coastal stewardship. The Reserve also offers opportunities for public access and is home to an award-winning visitor’s center. The property features several well-maintained hiking trails and has boardwalks, a wildlife viewing blind, and a fully-accessible scenic overlook.
The Elkhorn Slough NERR, is a component of the National Estuarine Research Reserve System (NERRS), a federal state partnership of protected research and education sites administered by the National Oceanic and Atmospheric Administration (NOAA) and the California Department of Fish and Game (CDFG). The NERRS was created in the legislation that established by the Coastal Zone Management Act (CZMA). As such the reserves are required by Federal regulation, 15 C.F.R. Part 921.13, to have a NOAA-approved management plan that is updated every five years. The Elkhorn Slough NERR Management Plan 2007-2011 meets the Reserve’s Federal obligation.
Within the plan we describe the Reserve’s long-term conservation goals and detail the process involved in identifying those goals. We also map out the objectives and strategies that the Reserve will use over the next five years in order to move toward accomplishing our goals. Furthermore, the plan gives an overview of our research and monitoring, education, stewardship, Coastal Training, volunteer, and administration programs and describes our plans for public access, acquisition, and facilities.
This plan is a significant revision of the original management plan that was approved by the California Department of Fish and Game (CDFG) and the National Oceanic and Atmospheric Administration (NOAA) in 1985. In developing this plan the Reserve used a collaborative approach, which focused on integrating the Reserve’s programs in order to better achieve conservation success.
Mission, Vision and Beliefs of the Elkhorn Slough NERR

The Elkhorn Slough NERR’s Mission, Vision, and Beliefs are as follows:


To improve the understanding and stewardship of Elkhorn Slough and its watershed.


The Elkhorn Slough NERR is a hub of substantive research, education, and resource management which models:

  • biodiversity through the protection of existing native habitat and the restoration of disturbed habitat through adaptive management practices

  • quality, hands-on interaction with watershed habitats without significant negative impact on the environment

  • inspiration of diverse audiences to make personal commitments to environmental stewardship

  • objective and responsible information exchange, interaction, and learning

  • broad-based community involvement

  • sound, up-to-date, and fiscally responsible infrastructure

  • high professional standards by staff and volunteers

  • long-term strategic planning

Statement of Beliefs

The Elkhorn Slough NERR Believes that:

  • Global environmental health depends on widespread commitment to stewardship, both individually and collectively

  • As an integral part of a natural system, the Reserve should maintain a watershed perspective.

  • Conservation best served when education, research, and resource management are interdependent and mutually supportive.

  • Reserve education should reflect best educational practice.

  • Everyone has the capacity to increase their knowledge and appreciation of the environment.

  • Reserve research should adhere to the highest standards of scientific inquiry.

  • Research should be widely accessible and results should be disseminated in a manner which is timely, clear, accurate, and unbiased.

  • Research should guide resource management decisions.

  • Optimal management of the Reserve contributes to long-term global environmental health.

Management Plan Planning Process

Most of this plan focuses on the Elkhorn Slough NERR’s long-term conservation goals and what the Reserve will do over the next five years in order to move closer to achieving those goals.

In developing these watershed-specific conservation goals we combined Reserve-developed methodologies with tools developed by the disciplines of conservation planning and program design in a novel approach we hope will provide future direction to Reserve staff and their conservation partners. We first used extensive staff expertise and existing data to create a conservation assessment, which helped us to prioritize conservation targets. We then analyzed those targets to ascertain their predominate stresses and overall threats. Finally, we developed a comprehensive list of all of the actions needed to address stresses and threats and prioritized those actions which we felt could be achieved in the next 5 years.
ESNERR Conservation Goal #1

Protect and Restore Estuarine Habitats in the Watershed

The Elkhorn Slough NERR sits on the edge of a large estuary with habitats that include productive salt marshes, rich mudflats, and meandering tidal channels and creeks. Dozens of vascular algae and plant species, over 100 fish species, over 135 bird species, and over 550 invertebrate species have been reported from Elkhorn Slough’s estuarine habitats (Caffrey et al. 2002).

While Elkhorn Slough today still hosts extensive estuarine habitats and diverse species, there is strong evidence that local biodiversity is threatened, and has already undergone significant changes in the past centuries (Caffrey et al. 2002). Over the past 150 years, human actions have altered the tidal, freshwater, and sediment processes which are essential to support and sustain Elkhorn Slough’s estuarine habitats.
This has led to substantial changes in the extent and distribution of different estuarine habitat types. Major threats to estuarine habitats result from increased rates of tidal erosion, marsh drowning, and dikes. The accelerated rate of bank and channel erosion in Elkhorn Slough is causing tidal creeks to deepen and widen reducing functions for estuarine fish, salt marshes to collapse into the channel and die, and soft sediments that provide important habitat for invertebrates to be eroded from channel and mudflat habitats. Increases in the flooding of tidal waters on marshes are causing plants to “drown” in central areas of the marsh. Based on current knowledge, the accelerated rates of tidal erosion and marsh drowning are primarily due to the estuarine mouth modifications. Since the 1870s, approximately 30 percent of the salt marsh has been lost due to the construction of levees to drain wetlands for cattle grazing, railroad and road construction, and the creation of freshwater impoundments for duck hunting (Van Dyke and Wasson 2005). After a harbor was constructed at the mouth of Elkhorn Slough in 1947, 50 percent of the salt marsh was lost due to the marsh drowning and bank erosion and continues today at dramatic rates (Van Dyke and Wasson 2005). Tidal creek, mudflat, and channel habitats are also degraded by tidal erosion, which results in approximately two million cubic feet of sediment being exported from Elkhorn Slough each year. Reserve staff are leading a large, collaborative effort, the Elkhorn Slough Tidal Wetland Project (TWP), with the assistance of many partners to develop specific recommendations to conserve and restore estuarine habitats and implement them.
Other habit modifications of the Elkhorn Slough come in the form of invasive species. About 60 non-native invertebrates have been documented at Elkhorn Slough, and they include some of the most common species encountered, such as the European Green Crab and the Japanese Mud Snail (Wasson et al. 2001). There are also common algal, plant, and fish invaders in Slough estuarine habitats. Between the 1930s and 1970s, the majority of these invaders probably arrived with shipments of non-native oysters that were cultured at the Slough. Since then, the main introduction route is via hull-fouling on small boats traveling to Moss Landing Harbor. Most of the species arriving in recent decades first became established in San Francisco Bay (to which they were introduced largely by commercial shipping), then spread via boat traffic as well as natural transport of larvae on currents up and down the coast (Wasson et al. 2001). Marine and estuarine invasions have been shown to cause local extinction of native competitors and prey organisms, alteration of community composition and food webs, change in physical habitat structure, and even alteration of flow of energy and materials through whole ecosystems (Grosholz 2002).
In order to protect and restore estuarine habitats in the watershed the Reserve will work toward the following objectives over the next five years:

  • Restore and Enhance Estuarine Habitats with Restricted Tidal Flows

  • Reduce Erosion in Subtidal Habitats and the Loss and Degradation of Intertidal Habitats

  • Prevent new biological introductions into estuarine habitats

  • Detect and eradicate new biological introductions into estuarine habitats

  • Develop restoration strategies that help favor dominance by native assemblages

ESNERR Conservation Goal #2

Protect and Restore the Watershed’s Key Freshwater Habitats

Freshwater wetlands occur where land surfaces are saturated or covered by freshwater for sufficient time that the resulting plant community has adaptations to survive these stressful conditions. In the Elkhorn Slough watershed, freshwater habitats occur as riparian corridors, wet meadows, freshwater marshes, and ponds.

Freshwater habitats provide important habitat for diverse communities of plants and animals, including sensitive species such as the Santa Cruz Long-toed Salamander (Ambystoma macrodactylum croceum), California Tiger Salamander (Ambystoma californiense), California Red-legged Frog (Rana draytonii), and the Southern Pacific Pond Turtle (Actinemys marmorata pallida). Unfortunately, freshwater habitats have experienced significant losses over the last 150 years. A network of shallow lakes and freshwater marshes that once extended from south of the city of Salinas to north of the city of Watsonville was drained in the late 1800s and early 1900s for agriculture (Gordon 1996). A series of small upland ponds just north and south of lower Moro Cojo Slough was converted to agricultural and industrial land (Johnson and Rodgers 1854). Freshwater springs and seeps that were once common along the edges of Elkhorn Slough have been lost since the 1940s, presumably due to lowered groundwater levels resulting from agricultural and domestic pumping (Van Dyke and Wasson 2005).
Some freshwater habitats do remain in the watershed, but most face at least some level of ongoing threat. In many cases, exotic plants invade native plant communities, and introduced fish and amphibians prey upon threatened and endangered animals. In other cases, ponds, marshes and meadows are affected by excessive agricultural runoff which results in sediment accumulation, increased turbidity, and other pollutants. Furthermore, many of the watershed’s ponds are man-made, created from former salt marshes or seasonal streams, or otherwise excavated to form sediment basins or stock ponds. Presumably the hydroperiod, vegetation, and sediment characteristics of these waterbodies are quite different than the original freshwater wetlands that have been lost. The subsequent changes have influenced the plant and animal assemblages that currently inhabit these sites.
In order to protect and restore the watershed’s key freshwater habits the Reserve will work toward the following objectives over the next five years:

  • Maintain and enhance key freshwater habitats

  • Explore and act upon opportunities for watershed partnerships and outreach

  • Conduct research to improve management strategies for local freshwater habitats

  • Protect Reserve and key neighboring freshwater habitats from selected invaders

ESNERR Conservation Goal #3

Protect and Restore Maritime Chaparral is the Elkhorn Slough Watershed

Chaparral is perhaps California's most emblematic vegetation type, forming broad expanses across coastal and inland foothills and constituting about five percent of the state's land cover (Hanes 1988). Paradoxically, maritime chaparral, a manzanita-dominated association found only in relatively small patches near the coast, is one of our most uncommon and highly threatened vegetation communities. Significant stands of maritime chaparral remain in the Burton Mesa region of Santa Barbara County, near Morro Bay in San Luis Obispo County, and in the Monterey Bay area at former Fort Ord and on sandhills adjacent to Elkhorn Slough. Maritime chaparral is protected as environmentally sensitive habitat under the California Coastal Act and under Monterey County's Local Coastal Plan (Monterey 1982). Occurrences are mapped as a rare natural community by the California Department of Fish and Game in the California Natural Diversity Database (CNDDB).

Maritime chaparral patches in the Elkhorn Slough watershed occur within a matrix of coast live oak woodland, coastal sage scrub, and annual grassland as well as agricultural and rural residential development. Maritime chaparral is threatened by removal and fragmentation due to development, encroachment by invasive exotic species such as pampas grass, iceplant, and blue gum eucalyptus, and gradual conversion to other habitat types, particularly live oak woodland.
Today, approximately 2800 acres of maritime chaparral remain in north Monterey County. Of this, 1700 acres (61%) are within the boundaries of the Elkhorn Slough watershed. Of the watershed’s maritime chaparral, 350 acres (21%) are within conservation lands protected by ESF and The Nature Conservancy and 160 acres (9%) are within Manzanita County Park. The remaining 1190 acres (70%) are in either developed or as yet undeveloped parcels on privately owned land.
Because we only protect what we know and understand, the key to preserving remaining maritime chaparral is developing a network of watershed residents, educators, land managers, land-use decision makers, and scientists who are familiar with chaparral ecology and with policies and practices designed to protect and restore the habitat. This understanding will need to be developed in the visitor center and the classroom, in the laboratory and greenhouse, in the homes and gardens of watershed residents, and in the wild.

In order to protect and restore the watershed’s maritime chaparral habits the Reserve will work toward the following objectives over the next five years:

  • Preserve existing maritime chaparral in the Elkhorn Slough watershed

  • Reduce loss of maritime chaparral due to habitat type conversion

ESNERR Conservation Goal #4

Protect and Restore the Watershed’s Coastal Prairie and Coastal Scrub Habitats

Coastal prairie and northern coastal scrub are part of a complex and dynamic mosaic of upland habitats within the Elkhorn Slough watershed. Coastal prairie is a species-rich habitat that occurs within 100 kilometers of the coast. It hosts not only array of insects, amphibians, reptiles, birds, and mammals, but also a number of endangered annual forbs. This habitat can be defined, in part, by its native grass and forb species. Coastal prairie often coexists with, and frequently has a successional relationship with, northern coastal scrub (Ford and Hayes in press, Heady et al. 1988, Heady et al. 1992). Coastal scrub is an assemblage of evergreen shrubs, and within California, ecologists recognize northern and southern divisions. Northern coastal scrub occurs from Santa Barbara County north to the Oregon border. In the Elkhorn Slough watershed it is dominated by coyote brush. Co-dominants include California sagebrush, black sage, coffeeberry, bush monkeyflower, California blackberry, yellow bush lupine, and poison-oak. This habitat is important for a variety of small mammals and birds. The mosaic and herbaceous height characteristics of coastal prairie with northern coastal scrub are critical to the upland habitat quality for special-status species, including:

  • Santa Cruz sunflower (federal and state listed endangered),

  • artist's popcornflower (California Native Plant Society 1B: Rare, threatened or endangered in California and elsewhere 1B),

  • peregrine falcon (state listed as endangered),

  • northern harrier (species of special concern),

  • Santa Cruz long-toed salamander (federally and state listed as endangered),

  • California red-legged frog (federally listed as threatened), and

  • California tiger salamander (species of special concern) (CalPIF 2004, Becker 1988, L. Ford pers. comm., Hobbs and Mooney 1986).

Unfortunately, both coastal prairie and coastal scrub face significant threats. Approximately 99% of California native grasslands have been lost over the last 200 years, making them one of the most critically endangered ecosystems in the U.S. (Noss et al. 1995). Loss of coastal scrub in some parts of California has also been severe. Up to 90 % of the historic acreage of southern coastal scrub has been lost to development (Noss et al., 1995). Northern coastal scrub is apparently more secure for now, but it too has declined by over 35% since 1950 (FRRAP 1988:Table 7-4; FRAP 2003), and faces the same sprawl as Southern California. Within the Elkhorn Slough watershed, coastal scrub assemblages often face threats from infestation by tall exotic biennials and perennials, such as poison hemlock, fennel, and jubata grass.

Despite dramatic losses locally and statewide, some remnant coastal prairie and intact coastal scrub persists in the Elkhorn Slough watershed and on the Elkhorn Slough NERR. The Reserve will give priority to identifying and preventing the establishment of new invasive exotic plants in these areas on the Reserve.
In order to protect and restore the watershed’s coastal prairie and costal scrub habits the Reserve will work toward the following objectives over the next five years:

  • Reduce abundance of selected non-native plant and animal species in Reserve coastal prairie and coastal scrub assemblages.

  • Help build support for regional Coastal Prairie and Coastal Scrub projects.

  • Implement research that informs regional restoration strategies

ESNERR Conservation Goal #5

Protect and Restore the Watershed’s Coast Live Oak Habitats

Coast live oak (Quercus agrifolia) woodland is common in the Elkhorn Slough watershed and is often found growing on 15 to 50 percent slopes and loamy sands in the hills east of the Elkhorn Slough National Estuarine Research reserve (Elkhorn Slough NERR). On the Reserve, oak woodlands also frequently appear on the slopes of dissected terraces. Oak woodland can range from dense forests with closed canopies at moderately moist sites, to widely-spaced open woodland or savannah in drier areas. Oak understory vegetation is also variable. Where the canopy is closed, understory vegetation often includes shade-tolerant shrubs, ferns, and forbs. Where trees are scattered, the understory is commonly made up of grassland and occasional shrubs (Holland 1988). At Elkhorn Slough NERR, the overstory is made up exclusively of coast live oak, and common native understory species include poison oak (Toxicodendron diversilobum), sword fern (Polystichum munitum), California blackberry (Rubus ursinus), hedge nettle (Stachys bullata), snowberry, (Symphoricarpos albus var. laevigatus), coffeeberry (Rhamnus californica and R. tomentella), beeplant (Scrophularia californica) and miner’s lettuce (Claytonia perfoliata). Creeping wildrye (Leymus triticoides) and Santa Barbara sedge (Carex barbarae) also occur in open woodlands.

Coastal oak woodlands provide habitat for a variety of wildlife species, including many mammals and a wide range of birds. According to California Partners in Flight and the Point Reyes Bird Observatory (2002), oak woodlands have the richest wildlife species abundance of any habitat in California, and may rank among the top three habitat types in North America for bird richness. The California Wildlife Habitat Relationships System lists over 200 animals species that live in or otherwise use coastal oak woodlands in Monterey County. In the Elkhorn Slough watershed these include nesting white tailed kites (California Fully Protected) and golden eagles (California Species of Special Concern), Swainson’s hawks (California Threatened), peregrine falcons (California Endangered), and seasonally, Santa Cruz long-toed salamanders (Federally and California Endangered).
It is unknown how many oaks in the Elkhorn Slough watershed have been lost over the last 150 years. Comparisons between mid-nineteenth century surveys and recent aerial photos hint at large-scale changes. When surveying the boundaries of Spanish land grants and township and range lines in the 1850s and 60s, the U.S. Surveyor General mapped many natural features, including oak trees. In the Elkhorn Slough watershed, oaks were therefore mapped on the boundaries of the San Cayetano, Los Carneros, and Bolsa Nueva y Moro Cojo ranchos, and along the public lands north of Hall Road, on the Springfield Terrace, and in the hills approximately 3.5 kilometers east of today’s Elkhorn Slough NERR. Only half of the survey points shown as coast live oak in the 1800s are oak habitat today. Approximately 40% of the originally mapped oaks have since been converted to agricultural fields or grassland, while the other approximately 10% have since been replaced by non-native eucalyptus or pine trees (U.S. Survey General 1872, Foreman 1867, Terrell 1859, Day 1854, Freeman 1854).
In order to protect and restore the watershed’s coast live oak habits the Reserve will work toward the following objectives over the next five years:

  • Protect the watershed’s coast live oak habitats from biological invaders.

  • Investigate the habitat use of native oak vs. non-native eucalyptus groves.

ESNERR Conservation Goal #6

Reduce Pollution across the Elkhorn Slough Watershed

Estuaries often have particularly high levels of pollution relative to other coastal habitats, because human uses such as industry, agriculture, residential development, and harbors are often densely concentrated around them (Kennish 2002). In estuarine habitats of the Elkhorn Slough watershed, numerous contaminants from a variety of sources have been identified, and many more no doubt remain undetected. In this largely rural watershed, the main cause of water and sediment quality degradation appears to be agricultural non-point source pollution (Caffrey 2002, Phillips et al. 2002).

The Elkhorn Slough National Estuarine Research Reserve’s (Elkhorn Slough NERR) water quality monitoring program has documented elevated nutrient levels in watershed wetlands. For instance, in the South Harbor, Tembladero Slough, and old Salinas river channel, nitrates average over 50 mg/L (vs. safe drinking water standard of 10 mg/L), and the peak values at these sites are among the highest ever reported for estuarine ecosystems (Caffrey 2002). In the main channel of Elkhorn Slough, nitrate concentrations are lower, averaging 5 mg/L or less. However even in these areas strongly flushed by the tides, higher concentrations occur in the rainy season, partly due to subwatershed sources. This is shown through data generated for National Estuarine Research Reserve’s System-wide water quality program, which sometimes detects much higher level of nutrients in Reserve wetlands on outgoing tides, attributable to local sources, than on incoming tides. Furthermore, an array of in-situ nitrate monitoring instruments has recently documented nitrate from Salinas River channel / Tembladero Slough sources traveling up the Slough, into and well past the Reserve (K. Johnson in prep;
In order to reduce pollution across the Elkhorn Slough Watershed the Reserve will work toward the following objectives over the next five years:

  • Improve understanding of pollution levels, sources, and effects on coastal habitats.

  • Generate and disseminate information on estuarine values and how they are affected by pollution.

  • Decrease effects of agricultural run-off and erosion on the Reserve.

ESNERR Conservation Goal #7

Monitor Key Indicators of Coastal Ecosystem Health to Enhance Understanding of Spatial and Temporal Variation and Long-term Trends

Long-term monitoring programs – those carried out consistently for at least a decade, and ideally many decades – are vital for detecting spatial and temporal trends in ecosystems, and for distinguishing natural from anthropogenic perturbations. Long-term datasets improve our understanding of, and thus decision-making about, complex ecological processes that occur at large spatial and temporal scales (Vos et al. 2000).

In the Elkhorn watershed, the Elkhorn Slough National Estuarine Research Reserve (Elkhorn Slough NERR) is ideally suited to designing and implementing long-term monitoring. There is strong institutional support at the local (Elkhorn Slough NERR) and national (National Estuarine Research Reserve System) level for carrying out high quality, consistent monitoring of key indicators of coastal health. The Reserve is committed to continuing its role as a leader in regional monitoring.
To improve the management of complex coastal ecosystems, it is important to use a combination of different indicators at multiple scales, from ecosystems to habitats to species (Noss 1990, Wilson 1994). Reserve monitoring programs fall into three main categories:

  1. Water quality and weather monitoring to characterize overall ecosystem health

  1. Habitat and land use change monitoring to track changes in the extent and distribution of different land cover classes, and

  1. Biological monitoring of threatened species and characteristic estuarine and coastal communities.

In order to monitor key indicators of ecosystem health in the watershed the Reserve will work toward the following objective over the next five years:

    • Collect, archive, and disseminate consistent, high caliber data on critical ecosystem characteristics.

The long-term monitoring programs are summarized in Tables 9.1 through 9.6.

ESNERR Conservation Goal #8

Educate the Community about the Watershed and Inspire Them to Consider Environmental Conservation When Making Decisions Affecting Elkhorn Slough and Its Watershed
The Reserve offers a mosaic of education programs that are designed to reach a variety of audiences through different venues using different delivery modes. Based on target audiences these programs can be grouped into four components:

  1. Coastal Training Program – reaching local and regional decision makers though workshops, workgroups, independent scientific review, distribution of information, and networking with experts.

  1. School Programs – current programs include: K-12 Teacher Professional Development, Reserve-based Field Experiences, Interactive Virtual Field Trips, Multicultural Outreach, K-12 and Non-formal Education Partnerships, and support of college and university courses, community service programs and student internships.

  1. Public Education – centering on the visitor center and five miles of trails, offering guided tours, special events, and opportunities for outreach to neighbors in the Elkhorn Slough watershed.

  1. Volunteer Program – trains a cadre of community volunteers to assist with the implementation of the other education programs and also serve to support the research, monitoring and restoration programs, and other aspects of the operation of the Reserve.

The challenge for the Reserve’s environmental education program is to offer entry level experiences for all ages with opportunities to take “courses” of greater depth and increasing levels of involvement.

In order to educate the community about the watershed and inspire them to consider environmental conservation when making decisions affecting Elkhorn Slough and its watershed the Reserve will work toward the following objective over the next five years:

    • Create and implement environmental education programs for school-aged children, visitors, our watershed neighbors, and decision makers.

ESNERR Conservation Goal #9

Maintain a Viable Base for ESNERR Programs: Organization, Budget, and Facilities

In order to successfully protect, restore, research, and educate, we must provide a strong organizational and infrastructure foundation upon which these activities can build. Important conservation goals can only be fully achieved when the staffs working on them have a productive and safe environment in which to work, as well as the resources and tools necessary to do their jobs. The rationale is simple: If an organization is plagued with unsafe or uncomfortable working conditions, low morale, bad communications, disorganization, too few funds, a poor public image, or inadequate facilities, it is less able to accomplish its mission.

In order to maintain a viable base for ESNERR programs the Reserve will work toward the following objective over the next five years:

    • Maintain a productive, safe, and efficient ESNERR work environment.

    • Maintain a visible and positive ESNERR image.

    • Maintain, repair, and construct ESNERR facilities and infrastructure.

Program Overviews


People and funding are the basis of all Reserve programs. If either one of these elements is missing or is mismanaged, the program will fail and conservation goals will not be attained. Operating in a well-organized manner increases efficiency and productivity. Positive public relations help garner funding, partnerships, and community support which, in turn, promotes Elkhorn Slough watershed conservation.

The administration program’s purpose is to provide human and fiscal resource management to the Reserve and to provide a framework of policies and processes necessary to support Reserve programs and operations.

  • To provide well-trained staff to achieve the Reserve’s conservation goals.

  • To provide a stimulating, healthy work environment for all staff.

  • To procure and responsibly manage funding to achieve the Reserve’s conservation goals.

  • To foster cooperation within and between CDFG, NOAA, and ESF.

  • To facilitate the development and implementation of clear policies and procedures to guide the management of the Reserve.

  • To operate the Reserve in a well-organized and efficient manner.

  • To provide high quality public information about the Reserve.

Volunteer Program

Reserve volunteers assist with the work of stewardship, research, education, public outreach, maintenance, and administration. Their hours represent a significant contribution to Reserve programs. Moreover, the Reserve converts volunteer hours into a dollar value which is then used as in-kind match for grants. In 2005, the financial value of volunteer hours to the Reserve was over $100,000.

Some of the benefits of a volunteer program are less directly tangible than a dollar value represented by their hours worked. Well-trained and enthusiastic volunteers serve as important community ambassadors for conservation. It has been shown that volunteer programs are needed by society to provide a venue for like-minded people to get together and share their passion for a cause. Providing those opportunities, in the context of working toward important conservation goals, is part of what the Elkhorn Slough volunteer program can provide.

The purpose of the volunteer program is to recruit, train, and support volunteers so they can effectively assist Reserve and ESF staff in carrying out their conservation goals. Our core belief is that knowledge of and appreciation for nature precedes and motivates conservation behavior.

Program Goals

  • Address the needs of volunteers

      • In order to be productive and have a positive personal experience, volunteers must enjoy what they do and feel appreciated.

  • Maintain a well-organized and well-managed volunteer program

      • Clear guidance must be given regarding issues such as policies, procedures, and minimum requirements for training and service. Accurate and up-to-date data bases of volunteer information, hours and type of service must be maintained.

  • Focus volunteer efforts on the highest priority needs of the Reserve and ESF

      • Annual evaluation of work plans of both staff and volunteers is necessary to insure that the most important tasks are being given the greatest effort.

  • Maintain high quality volunteer output

      • In order to insure that volunteers serve as appropriate and effective ambassadors for the Reserve and for watershed conservation, regular evaluation of their performance is necessary. Evaluation results will inform where training or feedback is needed and will guide future program planning.

Education Program

As environmental educators we are facing an increasingly complex challenge, an obligation of global significance, and an urgency that requires us to be thoughtful and strategic in our efforts. Some of these challenges include:

  • The population of California is incredibly diverse, with over 50 different languages spoken in the public schools, (Jepsen 2005) and is expected to increase by 11.3 million to a total of 45 million people by the year 2020, (CDOF 2001). Likewise, the Monterey Bay Area will see a population increase of over 130,000 people by 2020 and another 156,000 people will arrive by 2050 (Figure 16.1) (State of California, Dept of Finance 2004). These people will be neighbors to the Elkhorn Slough and many will inevitably live in its watershed.

  • California is also home to one third of “at risk species” identified in the United States. The state is considered to be one of the 25 most significant biological hotspots in the world (Stein 2000). There are twenty-one threatened or endangered species in the Elkhorn Slough and neighboring Pajaro and Salinas River watersheds.

  • Our terrestrial activities are linked to the world’s ocean through watersheds and estuaries and have had significant detrimental effects. Recent reports from the US Commission on Ocean Policy (2004) and the Pew Oceans Commission (2003) have made it abundantly clear that the ocean and coastal habitats are in dire need of increased study and protection.

The core effort of our education program must continue with even greater urgency as the population encroaches; people become more urbanized and divorced from nature; and social, political and economic forces converge in the next decade to determine what will be left of the natural systems in the watersheds of the central coast.


The Reserve’s education programs are designed to address different issues within different time frames. We strive to strategically define priorities and develop programs that address:

  1. The most immediate threats to coastal habitats and the people (decision makers) who most need to understand the issues in order to make well informed decisions. This time frame includes targeted CTP workshops.

  1. The issues on an intermediate time frame that require the building of a baseline of understanding among professionals in both private and public sectors, public servants (politicians) and the general public who can get involved in the community decision making process, (public hearings, planning commissions, general plan updates). The Reserve education program can help by defining specific research needs, and/or by defining and interpreting existing research so people can be involved in discussions in the larger community pertinent to making well informed decisions. This time frame includes professional development, a second tier of CTP workshops, graduate level research, student internships, and collaborations with college level course instruction.

  1. The long-term need of providing quality K-12 education programs to develop a culture of conservation that includes

      1. an awareness, appreciation for and understanding about nature

      2. experience with scientific inquiry and appreciation for the strengths and limits of science

      3. an understanding of career choices and the education required to work in these careers

      4. an understanding of the decision making process, power structures in the community and a desire to be involved in shaping the local landscape.

This time frame includes teacher professional development, curriculum development and field experiences for K-12 students.

To achieve ESNERR’s conservation goals outlined in previous chapters, our programs must continually adapt to a rapidly changing world to meet high standards of excellence in content and presentation. The critical information and experiences we provide must be clearly defined, the audiences understood, and the two brought together in carefully choreographed workshops, forums, events and activities with the use of appropriate communication mediums and technologies.

We strive to develop flexible, responsive programs of clearly defined geographical scope, integrated with the activities/programs of local partners, anchored by the needs of the local community (both human and non-human) and tied to the goals of our state and federal partners/agencies. The education staff has acquired expertise in defining the process of developing and maintaining such adaptive programs through the development of the Coastal Training Program. As a national program, the CTP is able to access national resources and apply them to very specific local needs. The CTP operational model includes the following components, which guarantee program success:

  • Ongoing market analysis that help identify key audiences and subjects not

targeted by similar programs;

  • Needs assessments that identify specific needs of target audiences;

  • A carefully chosen advisory committee that ensures communication with key

partners and networking with appropriate agencies and professionals in the


  • Strategic planning that provides vision while articulating the unique niche that the

Reserve fills in the region;

  • Short and long-term performance measures that help to track success and improve programs.

Aspects of this model are being applied to the other elements of the education program. (see Chapter X for details)

Research Program

To better fulfill our role as coastal stewards, we need to better understand the complex process and dynamics of our estuarine watershed and coastal biodiversity. We need to know more about the relative impacts of various potential threats and about the effectiveness of different restoration strategies. We need to better characterize the Slough’s biodiversity to understand which estuarine species need our special support, because of the key role they play or because of their rarity. Applied conservation research, while becoming more common, still comprises a tiny minority of the investigations conducted by academic institutions. The Elkhorn Slough National Estuarine Research Reserve (Elkhorn Slough NERR) thus plays a critical role in encouraging, supporting, and synthesizing applied conservation research by regional scientists. Furthermore, Reserve researchers themselves conduct original conservation research to address critical gaps in our understanding.


In order for coastal managers to make informed decisions, they must possess credible, relevant information about the systems and species under their charge. History has shown us what can happen when human actions, often with the best of intentions, are taken without proper knowledge of the consequences. Research is necessary to help insure the intended consequences are realized and to help minimize the risk of unintended consequences of human activities.


According to the CZMA, a key goal of the Reserves is to “conduct and coordinate estuarine research within the System, gathering and making available information necessary for improved understanding and management of estuarine areas.”

In order to meet this overarching coastal program goal, we strive to..

  • Detect short term variability and long term change in Elkhorn Slough and its watershed through various monitoring projects

  • Produce unbiased, scientifically robust data as a result of short-term applied conservation research

  • Disseminate data, reports, theses, research conclusions, and other relevant scientific information about Elkhorn Slough available

  • Facilitate and encourage research to fill the highest-priority data gaps

  • Encourage research by outside scientists

  • Archive scientific information about Elkhorn Slough

Stewardship Program

California is a biological rich region, home to well over 4000 species of plants and almost 600 species of vertebrates (Myers et al 2000), but most of the state’s natural ecosystems face serious anthropogenic threats. California has been designated a biodiversity hotspot, or an area where exceptional concentrations of endemic species are undergoing exceptional losses of habitat (Myers et al 2000). These losses occur in two basic ways. The first is through conversion, or the outright change of natural habitat into developed or agricultural areas. The second is through qualitative losses which involve changes or degradation in the structure, function, or composition of an ecosystem. At some level of degradation, an ecosystem ceases to be natural (Noss et al. 1995). Losses due to both conversion and degradation have been significant. California native grasslands have been reduced to about one percent of their original extent, both through land conversion and degradation by exotic species invasions. Other seriously threatened ecosystems include wetlands and riparian woodlands, which have been reduced to 10 percent or less of their original area (Noss et al. 1995). Predictably, many of the animal species dependent on these habitats have declined as well.

The Elkhorn Slough watershed shares many of the same human impact issues as other habitats across the state and the nation. For example, the Elkhorn Slough National Estuarine Research Reserve’s (Elkhorn Slough NERR) grassland and oak woodland understories are, with few exceptions, highly degraded and invaded by exotic plants; its freshwater springs have been almost entirely lost due to groundwater overdraft; and 75% of its historical salt marshes have been lost through conversion, first to agricultural land, and later to mudflats and permanently subtidal lagoons. In order to preserve the natural habitats that remain, the Elkhorn Slough Reserve’s stewardship program gives high priority to habitat protection within Reserve boundaries. In areas already degraded by past land uses, invasive species, or pollution, the stewardship program endeavors to sustainably recover or restore at least some of the lost aspects of local biodiversity and natural processes.

The purpose of the Reserve’s stewardship program is to protect and restore coastal habitats in the Elkhorn Slough watershed, with emphasis on the Elkhorn Slough NERR. The stewardship staff works collaboratively with the Reserve research and education staff to design and implement a number of projects including invasive species control, endangered species management, habitat mapping, ecological restoration, erosion control, community outreach, and applied research. CTP often provides information critical to scientifically-sound project design, and Reserve volunteers are frequently instrumental in project implementation. Through these actions, the stewardship program helps to protect and rehabilitate the diversity and integrity of native species and communities natural to the region. The main components of the stewardship program are briefly described below.


The Reserve’s key stewardship goals are to:

  • Protect intact, native habitats and sensitive species

  • Restore degraded conservation targets

  • Manage habitats that require ongoing manipulation

  • Use restoration science and or adaptive management techniques that allow us to share, scientifically, with other land managers which techniques work, and which do not.

Operations and Facilities Program

It is difficult and sometimes even impossible to achieve many conservation goals without a healthy physical infrastructure in place. Buildings, roads, and parking areas must be built and maintained in order for basic activities to take place. Providing researcher and public access as well as interpretive services presents another suite of physical site needs and an increased responsibility to public health and safety.

Some operations and facilities activities overlap strongly with the Stewardship Program. For example, managing weeds is important for both improving native habitat and for fire protection.

The purpose of the operations and facilities program is to provide a stable foundation of infrastructure upon which the Reserve’s research, education, stewardship, and administration programs can succeed.


Elkhorn Slough NERR will strive to plan, construct, and operate facilities that:

  • are well-maintained, attractive, safe, and fully-functional,

  • comply with the requirements of the Americans with Disabilities Act,

  • support multiple Reserve goals,

  • minimize environmental impacts.

Chapter I.


This document is the second edition of the management plan for the Elkhorn Slough National Estuarine Research Reserve (Elkhorn Slough NERR), and covers the period from 2007-2011. This plan is a significant revision of the original management plan that was approved by the California Department of Fish and Game (CDFG) and the National Oceanic and Atmospheric Administration (NOAA) in 1985.

The first iteration of the management plan was developed after inclusion of the Elkhorn Slough NERR into the National Estuarine Research Reserve System (NERRS). During the development of the 1985 plan the Reserve was still in its infancy with most of its programs still just concepts on paper. However, over the last 20 years, through the hard work of many individuals, the Reserve has steadily evolved. Today the Elkhorn Slough NERR supports fully-functioning research, education, coastal training, and stewardship programs that are making significant contributions to the conservation of the estuary and its watershed. But the environmental threats facing the Reserve and the surrounding watershed remain great and there is still much work to be done.
A. Purpose and Scope of Management Plan

Federal regulations (15 C.F.R. Part 921.13) require each National Estuarine Research Reserve to have a federally-approved management plan that provides direction for the Reserve programs by identifying goals and objectives, management issues, strategies, and proposed actions for meeting established goals and objectives. Management plans provide the basis for evaluation of the reserve pursuant to Section 312 of the Coastal Zone Management Act (CZMA).

The Elkhorn Slough NERR 2007-2011 Management Plan provides an overview of the:

  • environmental threats facing the Elkhorn Slough NERR and its watershed,

  • long-term goals the Reserve has developed in order to mitigate those threats and achieve the Reserve’s Mission,

  • Reserve’s objectives and strategies to move these goals forward over the next five years.

This management plan has been developed in accordance with the regulations of CDFG and NOAA, including all provisions for public involvement. It is consistent with the congressional intent of Section 315 of the CZMA, as amended.

B. Description, Mission, and Goals of the NERRS

The National Estuarine Reserve System was created by the Coastal Zone Management Act (CZMA) of 1972, as amended, 16 U.S.C. Section 1461, to augment the Federal Coastal Zone Management (CZM) Program. The CZM Program is dedicated to comprehensive, sustainable management of the nation’s coasts.

The reserve system is a network of protected areas established to promote informed management of the Nation’s estuaries and coastal habitats. The reserve system currently consists of 27 reserves in 22 states and territories, protecting over one million acres of estuarine lands and waters.

NERRS Mission

As stated in the NERRS regulations, 15 C.F.R. Part 921.1(a), the National Estuarine Research Reserve System mission is:

the establishment and management, through Federal-state cooperation, of a national system of Estuarine Research Reserves representative of the various regions and estuarine types in the United States. Estuarine Research Reserves are established to provide opportunities for long-term research, education, and interpretation.


Federal regulations, 15 C.F.R. Part 921.1(b), provide five specific goals for the reserve system:

(1) Ensure a stable environment for research through long-term protection of National Estuarine Research Reserve resources;
(2) Address coastal management issues identified as significant through coordinated estuarine research within the System;
(3) Enhance public awareness and understanding of estuarine areas and provide suitable opportunities for public education and interpretation;
(4) Promote Federal, state, public and private use of one or more Reserves within the System when such entities conduct estuarine research; and
(5) Conduct and coordinate estuarine research within the System, gathering and making available information necessary for improved understanding and management of estuarine areas.

National Estuarine Research Reserve System Strategic Goals 2005 – 2010

The reserve system began a strategic planning process in 1994 in an effort to help NOAA achieve its environmental stewardship mission to “sustain healthy coasts.” In conjunction with the strategic planning process, the Estuarine Reserves Division (ERD) and reserve staff have conducted a multi-year action planning process annually since 1996. The resulting three-year action plan provides an overall vision and direction for the reserve system. As part of this process, the reserve system developed a vision: Healthy estuaries and watersheds where coastal communities and ecosystems thrive; and mission: To practice and promote coastal and estuarine stewardship through innovative research and education, using a system of protected areas. The following goals are outlined in the 2005-2010 Strategic Plan.


  1. Strengthen the protection and management of representative estuarine ecosystems to advance estuarine conservation, research and education.

  1. Increase the use of reserve science and sites to address priority coastal management issues.

  1. Enhance peoples’ ability and willingness to make informed decisions and take responsible actions that affect coastal communities and ecosystems.
Biogeographic Regions

NOAA has identified eleven distinct biogeographic regions and 29 subregions in the U.S., each of which contains several types of estuarine ecosystems (15 C.F.R. Part 921, Appendix I and II). When complete, the reserve system will contain examples of estuarine hydrologic and biological types characteristic of each biogeographic region. As of 2006, the reserve system includes 27 reserves and two reserves in the process of designation. The reserves are listed below by biogeographic region and subregion with their designation date denoted in parentheses (Figure 1.1).

Acadian – Southern Gulf of Maine

1. Wells Reserve, Maine (1984)

2. Great Bay Reserve, New Hampshire (1989)

Virginian - Southern New England

3. Waquoit Bay Reserve, Massachusetts (1988)

4. Narragansett Bay Reserve, Rhode Island (1980)
5. Hudson River Reserve, New York (1982)
Virginian – Middle Atlantic

6. Jacques Cousteau Reserve, New Jersey (1998)

7. Delaware Reserve (1993)
Virginian – Chesapeake Bay

8. Chesapeake Bay Reserve, Maryland (1985,1990)

9. Chesapeake Bay Reserve, Virginia (1991)
Carolinian – North Carolina

10. North Carolina Reserve (1985,1991)

Carolinian – South Atlantic

11.North Inlet-Winyah Bay Reserve, South Carolina (1992)

12. ACE Basin Reserve, South Carolina (1992)
13. Sapelo Island, Georgia (1976)
Carolinian – East Florida

14. Guana Tolomato Matanzas Reserve, Florida (1999)

West Indian – West Florida

15. Rookery Bay Reserve, Florida (1978)

Louisianan – Panhandle Coast

16. Apalachicola Reserve, Florida (1979)

17. Weeks Bay Reserve, Alabama (1986)
Louisianan – Mississippi Delta

18. Grand Bay Reserve, Mississippi (1999)

Louisianan – Western Gulf

19. Mission-Aransas Reserve, Texas (2006)

Californian – Southern California

20. Tijuana River Reserve, California (1982)

Californian – Central California

21. Elkhorn Slough Reserve, California (1979)

Californian – San Francisco Bay

22. San Francisco Bay, California (2003)

Columbian – Middle Pacific

23. South Slough Reserve, Oregon (1974)

Columbian – Puget Sound

24. Padilla Bay Reserve, Washington (1980)

Great Lakes – Lake Erie

25. Old Woman Creek, Ohio (1980)

Great Lakes – Lake Ontario

26. St. Lawrence River, New York (Proposed)

Fjord – Aleutian Islands

27. Kachemak Bay Reserve, Alaska (1999)

West Indian – Caribbean

28. Jobos Bay Reserve, Puerto Rico (1981)

Figure 1.1. Map of the reserves and represented bioregions in the National Estuarine Research Reserve System.

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