Sanctuary Integrated Monitoring Network
Monterey Bay National Marine Sanctuary
Elkhorn Slough
Estuaries represent the confluence of terrestrial, freshwater and marine ecosystems, creating multiple unique habitats that support highly diverse communities and provide important ecosystem services. Unfortunately, these rare but highly productive areas are also very fragile, and human encroachment has compromised their ability to provide biological services (e.g., nursery and feeding grounds for fishes and birds) and has diminished their ability to act as an environmental filter.

During the course of the last century, human activities have altered local hydrology (e.g., with levees, dams, diversions) and impacted water and soil chemistry (e.g., with pesticides, pollutants), which in turn has negatively affected the biological communities within these systems.

In many parts of the world, estuarine habitats continue to disappear as they are converted into arable land for agriculture or to accommodate urban sprawl.

Within or immediately adjacent to the Monterey Bay National Marine Sanctuary there are 26 estuarine habitats identified by the U.S. Fish and Wildlife Service and listed in its National Wetlands Inventory. These listed habitats include an area in Pillar Point Harbor, Pescadero and Scott Creek marshes, four sloughs and 19 lagoons - all of which experience, at least seasonally, some mixing of fresh and salt water. The largest estuary in the sanctuary is Elkhorn Slough, which serves as an important resting and/or feeding stop for migratory species using the Pacific Flyway. Elkhorn Slough also serves an important role in sustaining resident birds that use the resources generated by this highly productive ecosystem.

Designated in 2000 as a Globally Important Bird Area by the American Bird Conservancy, Elkhorn Slough is world-renowned among avid bird watchers for its diversity and abundance of bird species. After San Francisco Bay, Elkhorn Slough has one of the largest remaining salt marshes in California. Its estuarine habitats host more than 100 fish and more than 400 invertebrate species as well as marine mammals, including dozens of southern sea otters.

In addition to habitat loss and alteration at the hands of human activities, estuaries are also threatened by invasive species. Often referred to as biological pollutants, invasive plants and animals have been introduced intentionally or accidentally since the arrival of humans.

In some cases, these species have displaced natives and altered ecosystem structure and function. However, for most of these invasive species, the long-term extent of their impact on estuaries remains unknown.

By 2001, researchers had already documented 56 invasive invertebrate species in Elkhorn Slough, making it the most invaded natural habitat within the sanctuary. In the high intertidal zone of the upper salt marsh, more than 30 invasive plants are also common.
Clapper Rail Rallus longirostris. Although the species is abundant in east coast marshes, the California subspecies is rare.

Highway 1 bridge over Elkhorn Slough.


Most of the estuary-related research conducted in the sanctuary takes place in Elkhorn Slough because it is the largest estuary within the sanctuary and it is adjacent to Moss Landing Marine Laboratories, a major academic research institution. It is also part of NOAA's National Estuarine Research Reserve System, a nation-wide network of protected areas established for long-term research, education and stewardship. Ongoing monitoring programs in Elkhorn Slough focus on water quality, bird censuses, nonindigenous species, and threatened and endangered species.

Monitoring estuaries is challenging because of the numerous habitats and incredible diversity of species found within them. For the same reasons, estuaries also present incredible opportunities to study physical, chemical and biological processes at multiple spatial scales and across different ecosystems (e.g., terrestrial, marine, freshwater). In addition, this information leads to testable hypotheses that will foster a better understanding of the mechanisms driving environmental change and how we can best alter human behavior to reduce our impact on these natural resources.

The Effect of the Moss Landing Power Plant Thermal Discharge Plume on the Distribution and Behavior of Sea Otters: a Preliminary Study
Southern sea otters, Enhydra lutris nereis, have occupied various parts of Elkhorn Slough over the past few decades. Recent observations of otters swimming in and adjacent to the thermal plume generated by the Moss Landing Power Plant served as the catalyst for this project. The study showed that otters were no more likely to occur at the thermal plume than the adjacent harbor mouth; and 95 percent of the observed behaviors were related to foraging.

The Influence of Varying Tidal Exchange on the Fish and Crab Assemblages of Elkhorn Slough
Alteration of freshwater and tidal influence through the construction of water-control structures (e.g., dikes, tide gates, culverts) is one of the most conspicuous and recent anthropogenic disturbances to Elkhorn Slough.

Communities were compared at dozens of sites with unrestricted vs. restricted tidal exchange. Overall, communities at sites with extremely restricted tidal exchange were markedly different from those with full tidal exchange. However, communities at restricted sites with moderate tidal exchange were only slightly different from those with full tidal exchange.

Full exchange appears to optimize native oysters, commercially valuable flatfishes, migratory shorebirds and site-level biodiversity. But minimal tidal exchange resulting from water-control structures supports a suite of estuarine endemic (native) species (including the tidewater goby and California brackish snail) not represented elsewhere and minimizes estuarine invasions. Total estuary-wide biodiversity may be enhanced with a mosaic of tidal exchange regimes.

Characterization of the Benthic and Planktonic Communities of Elkhorn Slough
Analyses of historical phytoplankton communities in Elkhorn Slough show that cryptophytes and diatoms, the two dominant planktonic communities, are inversely related. Cryptophytes are found in the upper slough waters, while the diatoms are near the slough mouth and indicate the strong marine influence there.

The separation of these planktonic communities remains in place, even though the exact locations move up and down the slough with the tides. Macrofaunal invertebrates continue to persist in the main channel, in spite of strong erosionally-driven modifications to substrate. Sea otters, which have increased recently, have not eliminated the slough prey in the same manner observed in similar sedimentary habitats. We believe this is related to the unique sediment refugia in the slough: hard clays exposed by erosion, shell debris and rocks scattered all around the mouth for erosion control. These are common deposits now and they are not easy to dig into.

Land/Ocean Biogeochemical Observatory (LOBO)
The aim of the LOBO project is to design and develop a real-time, in situ chemical sensor network for marine systems. With Elkhorn Slough as a test site, researchers measure nutrients such as nitrate, ammonium and phosphate, using instruments that allow for high-resolution sampling and the ability to access the data in near-real time.

For example, nitrate concentration in Moss Landing Harbor and at the L01 mooring provides an illustration of how the tidal cycle creates significant changes in water properties of the main channel of Elkhorn Slough. Hypersaline water from the upper slough can be seen at low tide, while the incoming tide brings nitrate into the slough.

Nitrate increases during high tide come from internal waves that bring deep, cold, nitrate-rich water from Monterey Bay to the nearshore surface, which then flows into the slough with the tidal bore. A second source of nitrate is the Old Salinas River, which enters the south end of Moss Landing Harbor and has nitrate concentrations as high as 1500 µM.

Long-Term Monitoring Programs of the Elkhorn Slough National Estuarine Research Reserve
The reserve conducts consistent long-term monitoring with rigorous standardized protocols and makes all data available to any individuals, researchers or organizations that request them. Monitoring programs fall into three areas:
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