Archived Workshops/References

Elkhorn Slough Water Quality



Elkhorn Slough, on the coast of the Monterey Bay, is located in a watershed with diverse land uses.  Approximately 25% of the land in the immediate watershed of the slough is in farm or ranch use.  Strawberries in particular are farmed on the terraces and slopes surrounding the estuary.  Moreover, the estuary receives inflow from the adjacent Tembladero and lower Salinas watersheds, through drainages that ultimately enter the estuary in south Moss Landing harbor.  Researchers at the Monterey Bay Aquarium Research Institute have documented that nutrients flowing from the old Salinas River channel through Moss Landing Harbor are swept up into the six-mile channel of the Elkhorn Slough estuary on incoming tides, accounting for the majority of nutrients detected there (Jannasch et al. 2008).  Nutrient concentrations in the estuary have been documented for decades, and at some sites near Moss Landing have exceeded levels detected in any other estuary worldwide.  While the ultimate solution to the effects of excess nutrients on the estuary is to reduce nutrient inputs, wetland managers can enhance local water quality by increasing tidal exchange to sites with tide gates or other water control structures.

The Coastal Training Program hopes that this portion of its website will serve as a clearinghouse on peer-reviewed literature relevant to the decision making on water quality in the Elkhorn Slough.  If you have suggestions to improve the website, please feel free to contact our office.   

Training Programs

Exploring Water Quality Trends and Connections: Tembladero-Lower Salinas-Elkhorn Slough Mar 19, 2012
Assessing Nutrient Loads in the Lower Salinas Sep 10, 2013
Water Quality and the Elkhorn Slough: A Tour for the Central Coast Regional Water Quality Control Board Nov 15, 2013
Historical Ecology and Water Quality Presentations to the Central Coast Water Quality Control Board Mar 7, 2014
Water Quality and the Elkhorn Slough: A Tour for the Central Coast Regional Water Quality Control Board Aug 28, 2014
Water Quality And The Elkhorn Slough: A Tour For The Central Coast Regional Water Quality Control Board Dec 12, 2014
Elkhorn Slough Water Quality Workshop Jun 2, 2015
Water Quality and the Elkhorn Slough: A Tour for the Central Coast Regional Water Quality Control Board Aug 27, 2015
Science of Nutrient Transport and Transformation in the Elkhorn Slough Estuary Mar 19, 2019
Elkhorn Slough Nutrient Modeling Contract to Assist in Developing the TMDL for Biostimulatory Substances Jul 9, 2019

Documents and Publications

Presentation: Water Quality: Trends and Concerns
PPT, 4.4MB
Mar 23 12
John Haskins
Elkhorn Slough National Estuarine Research Reserve
March 2012
Power Point presentation 3/19/2012
Coastal eutrophication as a driver of salt marsh loss
PDF, 1.3MB
Dec 13 13
Deegan, L.A., Johnson, D.S., Warren, R.S., Peterson, B.J., Fleeger, J.W., Fagherazzi, S. & Wollheim, W.M.
Nature 490:388-392
Here we present data from a nine year whole-ecosystem nutrient-enrichment experiment. Our study demonstrates that nutrient enrichment, a global problem for coastal ecosystems, can be a driver of salt marsh loss.
Diel Biogeochemical Cycling in a Hyperventilating Shallow Estuarine Environment
PDF, 1.6MB
Jan 04 12
Nicole G. Beck Kenneth W. Bruland
Estuaries 23(2):177-187
April 2000
The elevated biogeochemical cycling of oxygen, nitrogen, phosphorus, iodine, manganese, and iron found in this shallow estuarine environment suggest that tidal restrictions and anthropogenic nutrient enrichments can amplify diel variations and potentially hinder the functional and ecological stability of these systems. These data suggest that accurate chemical monitoring of the health of an estuarine ecosystem must account for the diel variability inherent in these highly productive environments.
Effects of upwelling on short-term variability in microbial and biogeochemical processes in estuarine sediments from Elkhorn Slough, California, USA
PDF, 502KB
Jan 04 12
Jane M. Caffrey, James T. Hollibaugh, Nasreen Bano, John Haskins
Aquatic Microbial Ecology 58:261-271
February 11, 2010
We examined short-term variability in sediment microbial processes and biogeochemistry in response to decreased irradiance accompanying an upwelling event.
High nutrient pulses, tidal mixing and biological response in a small California estuary: Variability in nutrient concentrations from decadal to hourly time scales
PDF, 653KB
Jan 04 12
Jane M. Caffrey, Thomas P. Chapin, Hans W. Jannasch, John C. Haskins
Estuarine, Coastal and Shelf Science 71:368-380
Biological processes had the greatest effect on nitrate concentrations during the dry season and were less important during the rainy season. While primary production was enhanced by nutrient pulses, chlorophyll a concentrations were not. We believe that the generally weak biological response compared to the strong physical forcing in Elkhorn Slough occurred because the short residence time and tidal mixing rapidly diluted nutrient pulses.
Identifying factors that influence expression of eutrophication in a Central California estuary
PDF, 390KB
Nov 03 11
Brent B. Hughes, John C. Haskins, Kerstin Wasson, Elizabeth Watson
Marine Ecology Progress Series 439: 31-43
October 20, 2011
Virtually every portion of the estuary shows impacts of over-enrichment by the high nutrient loads, ranging from thick algal mats to low night-time oxygen levels. The sites that show the most extreme symptoms are upstream of water control structures that restrict tidal exchange. These sites have low biodiversity, lacking the large fish or abundant shorebirds found in nearby sites with more tidal exchange. While the ultimate solution to the effects of excess nutrients on the estuary is to reduce nutrient inputs, wetland managers can enhance local water quality by increasing tidal exchange to sites with tide gates or other water control structures.
Nitrate Sources and Sinks in Elkhorn Slough, California: Results from Long-term Continuous in situ Nitrate Analyzers
PDF, 678KB
Jan 04 12
Thomas P. Chapin; Jane M. Caffrey; Hand W. Jannasch; Luke J. Coletti; John C. Haskins; Kenneth S. Johnson
Estuaries 27(5):882-894
Oct. 2004
The propagation of an internal wave carrying water from ~100 m depth up the Monterey Submarine Canyon and into the lower section of Elkhorn Slough on every rising tide was a major source of nitrate, accounting for 80-90% of the nitrogen load during the dry summer period.
Salt marshes and eutrophication: An unsustainable outcome
PDF, 1.6MB
Dec 13 13
Turner, R.E., Howes, B.L., Teal, J.M., Milan, C.S., Swenson, E.M. & Goehringer-Toner, D.D
Limnology and Oceanography 54(5):1634-1642
Enrichment reduces organic matter belowground and may result in a significant loss in marsh elevation equivalent to about half the average global sea level rise rates. Sustaining and restoring coastal emergent marshes is more likely if they receive less, not more, nutrient loading.
Signatures of restoration and management changes in the water quality of a central California estuary
PDF, 2.1MB
May 11 12
Gee, Alison Wasson, Kerstin Shaw, Susan Haskins, John
Estuaries and Coasts 33(4):1004-1024
Coastalmanagers and policy-makers are concerned with tracking improvements to water quality linked to management changes. Long-term water quality data acquired from two wetland areas in the upper reaches of the Elkhorn Slough estuary in central California were analyzed for signatures of land restoration or water control structure management. Post-restoration averaged NO3, NH3, and PO4 concentrations were 50-70% less than before-restoration concentrations. Assessment of watershed-scale effects revealed that proximity of restoration to sampling locations had almost as strong an effect on water quality as the percentage of land restored relative to watershed size. Results also suggest that restoration of even 1% of an agriculturally intensive watershed such as that of the Elkhorn Slough may result in improvements to water quality. Finally, results indicate that tide gate function can dominate water quality in managed wetlands and must be carefully tracked and managed in the context of estuarine conservation targets.
Spatial Variability in Nitrification Rates and Ammonia-Oxidizing Microbial Communities in the Agriculturally Impacted Elkhorn Slough Estuary, California
PDF, 1.1MB
Jan 04 12
Scott D. Wankel; Annika C. Mosier; Colleen M. Hansel; Adina Paytan; Christopher A. Francis
Applied and Environmental Microbiology 7(1):269-280
January 2011
Ammonia oxidation - the microbial oxidation of ammonia to nitrite and the first step in nitrification - plays a central role in nitrogen cycling in coastal and estuarine systems.
The Land/Ocean Biogeochemical Observatory: A robust networked mooring system for continuously monitoring complex biogeochemical cycles in estuaries
PDF, 2.3MB
Jan 04 12
Hans W. Jannasch, Luke J. Coletti, Kenneth S. Johnson, Stephen E. Fitzwater, Joseph A. Needoba, and Joshua N. Plant
Limnology and Oceanography: Methods 6:263-276
Up to five LOBO moorings have been simultaneously deployed and maintained in Elkhorn Slough, California, since November 2003. Continuous hourly data of biological, chemical, and physical properties are relayed to shore, processed, and disseminated to users through a web interface in near-real time. This article describes the design, implementation, and functionality of the LOBO monitoring system.
Using nitrate dual isotopic composition (d15N and d18O) as a tool for exploring sources and cycling of nitrate in an estuarine system: Elkhorn Slough, California
PDF, 1.7MB
Jan 04 12
Scott D. Wankel; Carol Kendall; Adina Paytan
Journal of Geophysical Research 114
This work expands our understanding of nitrogen and oxygen isotopes as biogeochemical tools for investigating NO3 sources and cycling in estuaries, emphasizing the role that cycling processes may play in altering isotopic composition.
Effects of Low Oxygen on Pacific Staghorn Sculpins and Olympia Oysters
PDF, 573KB
May 10 12
Van Parys, J. Rodriguez, M. Preisler, R. Haskins, J. Hughes, B. Wasson, K.
Elkhorn Slough National Estuarine Research Reserve; California State University, Monterey Bay; Hartnell College
October 2011
* Elkhorn Slough is an estuary in central California located in a productive agricultural watershed * The estuary hosts rich plant and animal communities, but monitoring has revealed that water quality at some sites is very impaired * Sites at Elkhorn Slough exceed limits for nutrient concentrations, algal cover, chlorophyll a, and dissolved oxygen (Hughes et. al) * A common ecosystem response from low dissolved oxygen is mortality of benthic organisms (Diaz and Rosenberg 2008) * For surviving organisms, they experience sublethal stressors including impacts on growth and reproduction (Vaguer-Sunyer and Duarte 2008) * No previous data has been collected linking water quality with estuarine species survival at Elkhorn Slough * We examined the effects of low dissolved oxygen on two common estuarine species
Nitrate Transport To Coastal Monterey Bay: Investigating Source Inputs From Elkhorn Slough
PDF, 5.1MB
Mar 27 12
Tanya Novak
Moss Landing Marine Laboratories; California State University Monterey Bay
Fall, 2011
Nitrate transport from Elkhorn Slough (ES) to the nearshore surface waters of Monterey Bay is examined using two years of time-series data from the Land-Ocean Biogeochemical Observatory (LOBO).....While rates of nitrate transport vary seasonally, assessment of nitrate transport mechanisms to coastal Monterey Bay in the summer to early fall is essential to understanding the dynamics of extreme algal blooms that typically occur during these months.
North Monterey County hydrogeologic study Volume II: Critical issues report and interim management plan
PDF, 8.8MB
Dec 18 13
Fugro West, Inc
Monterey County Water Resources Agency
The report describes the critical problems with water quality and quantity in the North Monterey County study area.
North Monterey County Hydrologic Study: Volume I Water Resources
PDF, 24.9MB
Jan 21 15
Fugro West, Inc
Monterey County Water Resources Agency
October 1995
Patterns and Causes of Variability in the Cover, Biomass, and Total Abundance of Ulva spp. in Elkhorn Slough, California
PDF, 655KB
Jan 04 12
Timothy J. Schaadt
M.S. Thesis from Moss Landing Marine Lab, Cal State Monterey Bay
August 2005
Although the affect of tides was not consistent among regions, my data indicate that tidal range can play an important role in the regulation of Ulva mats. Seasonal variability in algal mat dynamics occurred in Elkhorn Slough and some of these factors were also observed varying sub-seasonally potentially due to the effect of tides on Ulva mats.
Presentation: Proposed Nutrient TMDLs Lower Salinas River & Reclamation Canal Basin, & the Moro Cojo Slough Subwatershed Monterey County
PDF, 1.9MB
Feb 21 13
Pete Osmolovsky & Chris Rose Water Board TMDL Program
Central Coast Regional Water Quality Control Board
January 31, 2013
Statistical Analysis of Sixteen Years of Water Quality Data Project
PDF, 1.4MB
Jan 04 12
Marc Los Huertos
University of California at Santa Cruz
November 5, 2008
Water quality within Elkhorn Slough varies on both temporal and spatial scales. The trends at individual sites provide resounding support that monitoring water quality is a sensitive method of tracking ecosystem health. The source of variability, increasing turbidity, and elevated nutrient concentrations remains unknown.
Synthesis for management of eutrophication issues in Elkhorn Slough
PDF, 3.5MB
Jan 04 12
Brent Hughes
Elkhorn Slough Technical Report Series 2009:1
Evidence from other estuaries combined with data and observations from Elkhorn Slough over the last 40 years supports the idea that eutrophication is changing biological communities in Elkhorn Slough. The potential to reverse eutrophication through restoration projects in Elkhorn Slough remains uncertain, although limited data suggest some cause for optimism.
Water Quality Monitoring in Elkhorn Slough: a summary of results 1988-1996
PDF, 682KB
Jan 04 12
Jane Caffrey, Sue Shaw, Mark Silberstein, Andrew De Vogelaere, and Michelle White
Elkhorn Slough Technical Report Series 1997:1
May 25, 1997
Some trends we have observed from this data include: 1) a significant increase in nitrate concentrations since the 1970s 2) extraordinarily high nitrate concentrations in the lower Salinas River which may be the highest recorded in scientific literature for a river or estuary 3) concentrations of ammonium that are an order of magnitude lower (or more) than nitrate 4) low concentrations of dissolved oxygen in some areas which have restricted circulation 5) opening of the Salinas River lagoon leads to rapid increases in salinity in the lower river even during the rainy season when river discharge is high.


Researchers find high levels of mercury in coastal fog
Mar 30 12