Water Quality


The Monterey Bay National Marine Sanctuary provides habitat for a wealth of biological diversity, outstanding recreational opportunities and spectacular coastal scenery that is renowned on a world scale. Every organism that resides within or moves through the sanctuary depends upon clean water, as do all our commercial and recreational uses.

The sanctuary borders nearly 480 kilometers (300 miles) of California’s coastline and receives runoff from watersheds that cover approximately 18,130 square kilometers (7,000 square miles) and support a variety of land uses. The sanctuary is fortunate to be in an area with relatively few impacts from industrial discharges and large point sources of pollution. However, being adjacent to such a large extent of coastline makes it susceptible to impacts from non-point, urban, rural and agricultural pollution sources.

By the time rainfall or irrigation runoff enters streams, rivers, wetlands, estuaries and ultimately the sanctuary, it may contain high levels of nutrients, sediments or dangerous chemicals that have been picked up during the journey from land to sea. Monitoring has shown that while the sanctuary’s offshore areas are in relatively good condition, near-shore coastal areas, harbors, lagoons, estuaries and tributaries suffer from a number of problems, including elevated levels of nitrates, sediments, persistent pesticides, metals, bacteria, pathogens, detergents and oils.

These contaminants can have a variety of biological impacts, including bioaccumulation, reduced recruitment of anadramous species, algal blooms, mortality due to toxicity, transfer of pathogens to wildlife and humans, and interference with recreational use of the sanctuary.


To improve the water quality conditions in the sanctuary, it is important to understand fully where the pollution comes from, where it is going, what its impacts are and how water quality conditions are changing over time. To help address these issues, a number of ongoing water quality monitoring programs currently operate within the sanctuary and its watersheds. These include, among others:

  • The Central Coast Ambient Monitoring Program (CCAMP)
  • The Central Coast Long-term Environmental Assessment Network (CCLEAN)
  • The Sanctuary Citizen Watershed Monitoring Network
  • The Coastal Watershed Council (CWC)
  • Central Coast Watershed Studies (CCoWS) group
  • The US Geological Survey (USGS)
  • The Elkhorn Slough National Estuarine Research Reserve (ESNERR)
  • Santa Cruz and Monterey County Departments of Environmental Health
  • San Francisco Estuary Institute (SFEI)
  • The Granite Canyon Marine Pollution Lab

Together, these programs are gathering the data managers need to target source reduction efforts, assess trends and determine impacts.

The effects of human activities on water quality in Monterey Bay are both widespread and varied in the degree to which they disrupt the ecosystem and /or restrict water use. Monitoring and analysis have revealed high concentrations of nutrients, metals, pathogens, detergents and other contaminants in local creeks and rivers as well as in the numerous urban outfalls that drain into sanctuary waters.

As central coast populations grow, more pressure will be exerted on the sensitive ecosystems of Monterey Bay. Public awareness of these problems and an understanding of land use and management practices related to pollutant levels are important components of a strategy to improve water quality in these ecosystems.

The sanctuary’s Water Quality Protection Program (WQPP) educates the public about water quality issues and facilitates implementation of marine, urban and agricultural management practices to improve water quality. SIMoN has partnered with other monitoring organizations in the region to create an ongoing framework for data integration, regional water quality assessments and evaluation of management practice effectiveness.

Persistent Pesticides
Persistent pesticides are known to concentrate in the fats of wildlife; in high concentrations they can cause disease, lack of reproductive potential or mortality.

Toxic conditions that result from persistent pesticides have been shown to exist in the Pajaro River watershed (Hunt et. al., 1999), Salinas River watershed (Anderson et al., 2003; Hunt et al., 2002) and Santa Maria watersheds (Anderson et al., 2006). Contaminants are eventually transported to the ocean, where they can pose risks to human health and collect in the tissues of marine animals.

Recent studies have found high concentrations of persistent pesticides in mussels and sediments collected at The Hook in Capitola and Laguna Creek (CCLEAN Report, 2005). Concentrations of metals, such as copper and zinc, have been detected over the past few years in runoff from urbanized areas of Monterey that drain directly to the ocean (First Flush Report, 2005).

Legacy pesticides such as DDT bind to sediments and have been found concentrated at the coastal confluences with watersheds in our region. Excessive sedimentation can bury the gravel river bottoms where salmonids such as Coho and Steelhead spawn.

High nutrient loadings have been identified in Monterey Bay and may be attributed to nitrate runoff associated with fertilizer use in the area. High nitrate levels can result in harmful algal blooms with impacts to native species.

Over the past decade, ocean water has frequently exceeded standards for safe recreation due to bacterial contamination and the potential risk to human health posed by associated pathogens.

The contaminants often derive from runoff that comes directly from urban centers and rural residential areas through storm drains. These drains carry bacteria and detergents in part because of an aging sewer infrastructure.

Photo Library

Below is a sampling of related images found in the SIMoN Photo Library. Click or tap on an image for more details.

Map Repository

Cruise Ship Anchoring Sites

Cruise Ship Anchoring Sites

This map depicts permitted areas to anchor large cruise ships within Monterey Bay.
[View Larger]

Project Database


Analysis of mussels collected near the Moss Landing Power Plant thermal outfall

The National Oceanic and Atmospheric Administration (NOAA) Mussel Watch Program began in 1986 in order to evaluate pollutant load in U.S. coastal waters by sampling concentrations of contaminants in the tissues of mussels and oysters. In 2006, additional sampling sites were added in the Moss Landing Harbor in order to investigate any differences in contaminant concentrations between mussels near the thermal discharge site of the Moss Landing Power Plant and original Mussel Watch sites. Initial findings show that of the 11 heavy metals sampled, only concentrations of Cadmium (Cd) were found to be higher in mussels near the outfall pipe.


Center for Integrated Marine Technologies: Harmful Algal Blooms

Harmful agal blooms (HABs) are the result of rapid growth of toxin-producing unicellular algae. The toxins (e.g., domoic acid) can poison birds and mammals, close fisheries, and pose serious human health risks. The Center for Integrated Marine Technologies (CIMT) is using a variety of techniques to study this phenomenon.


Central Coast Ambient Monitoring Program

The Central Coast Ambient Monitoring Program (CCAMP) is the Central Coast Regional Water Quality Control Board’s regionally scaled water quality monitoring and assessment program.


Central Coast Long-term Environmental Assessment Network (CCLEAN)

CCLEAN provides the initial nearshore component of the Central Coast Regional Water Quality Control Board’s Central Coast Ambient Monitoring Program (CCAMP). This multidisciplinary program includes sampling in watersheds that flow into coastal regions, in estuarine coastal confluences, and at coastal sites.


Ecological Effects of the Moss Landing Thermal Discharge

This study was designed to provide a quantitative evaluation of the impacts of the thermal discharge into the Sanctuary from the Moss Landing Power Plant.


Effect of the Moss Landing Power Plant thermal discharge plume on the distribution and behavior of sea otters (Enhydra lutris nereis): a preliminary study

Southern sea otters (Enhydra lutris nereis) have occupied various parts of Elkhorn Slough over the past few decades. Recently, a large raft of otters has been noted just within the Moss Landing harbor entrance. In addition, some otters have been observed within and adjacent to the thermal plume generated by the Moss Landing Power Plant. This project studies sea otter behavior in and adjacent to the plume.


First Flush Event Monitoring by the Sanctuary Citizen Watershed Monitoring Network

First Flush occurs when the first sheeting rain of the season flushes roadways and impermeable surfaces, carrying months of accumulated contaminants and debris into the ocean.


Land/Ocean Biogeochemical Observatory (LOBO)

The LOBO observing system is designed to monitor the flux of nutrients (nitrate, phosphate and inorganic carbon) through the Elkhorn Slough ecosystem. The complete system will include up to eight nodes equipped with nutrient sensors developed at MBARI that are linked to the Internet through a wireless LAN (Local Area Network).


Literature Review To Characterize Environmental Contaminants That May Affect The Southern Sea Otter

The objectives of this study are to characterize environmental contaminants present in sea otter habitats that may affect population recovery, synthesize existing data on contaminant concentrations, and map their distribution.


Monterey Bay Aquarium Incoming Seawater Monitoring

As part of the Monterey Bay Aquarium’s ongoing water quality program incoming seawater is monitored with both spot measurements and continuously on a 5minute interval using in situ sensor technology. Both seasonal events, such as upwelling, and periodic events, such as El Niño are visible in the data record.


Monterey Bay Aquarium Nearshore Surface Seawater Bacteria Monitoring

The Monterey Bay Aquarium has been monitoring various aspects of near shore seawater quality including levels of bacteria since 1996.


Nearshore water monitoring of oxygen and pH in southern Monterey Bay

A decade-long time series of water quality parameters indicated that the nearshore, shallow subtidal was regularly inundated with cold, low oxygen and low pH waters.


NERR System Wide Monitoring Program

The National Estuarine Research Reserve System is a network of state-federal protected areas, representing diverse estuarine ecosystems. Elkhorn Slough NERR has 24 partner reserves that are located on both coasts of the US, as well as the Great Lakes and Puerto Rico. Since 1995 these 25 NERRs carry out consistent system-wide water quality and weather monitoring.


Nutrient Sources to Support the Gulf of the Farallones Food Web

The goal of this ongoing project is to determine whether nutrients from San Francisco Bay impact the rich food web of the Gulf of the Farallones in order to assess if anthropogenic changes in the estuary will have management implications for the coastal ecosystem.


Ocean Margin Ecosystems Group for Acidification Studies (OMEGAS)

This is a three-year, NSF-funded study on the impacts of acidic ocean waters on two ecologically important species (sea urchins and mussels) in the California Current Large Marine Ecosystem.


Santa Cruz County Beach Non-Point Pollution

Santa Cruz County Environmental Health Services (EHS) monitors county beaches and provides water quality information to concerned swimmers to alert them of possible areas that may be contaminated by fecal coliform bacteria.


Santa Cruz County Beach Water Quality

Santa Cruz County Environmental Health Service (EHS) has conducted regular testing of freshwater and saltwater swimming areas since 1968.


Santa Cruz Ocean Observing Platform (SCOOP)

The primary goals of the Santa Cruz Ocean Observing Platform (SCOOP) are to establish and maintain a long-term dataset of weather and oceanographic measurements at the Santa Cruz Wharf that is accessible to both researchers and the public.


Snapshot Day

Snapshot Day (SSD) is a one-day event that utilizes citizen volunteers to collect and analyze water samples from streams that enter the Monterey Bay National Marine Sanctuary (MBNMS). SSD began on the Central Coast on Earth Day 2000 and has become a widely recognized volunteer event in which important water quality information is gathered.


Southwest Ocean Outfall Regional Monitoring Program

The City and County of San Francisco owns and operates the Oceanside Water Pollution Control Plant that collects, treats to secondary standards, and then discharges municipal wastewater and storm water into the Pacific Ocean approximately 3.75 miles offshore of Ocean Beach.


Volunteer Water Quality in Elkhorn Slough

Elkhorn Slough National Estuarine Research Reserve , the Elkhorn Slough Foundation, and the Monterey County Resources Agency have been supporting a volunteer water monitoring program since 1988. Striking differences between sites and seasons were observed but significant long term changes over time are few.