Environmental Monitoring Program

Program Overview

The Environmental Monitoring Program (EMP) was established in 1971 to: 1) collect environmental data for resource management, 2) better understand estuarine processes, and 3) document compliance with water right decisions. EMP staff collect monthly water quality, chlorophyll, phytoplankton, benthic, and zooplankton samples at fixed locations in the Sacramento-San Joaquin Delta, Suisun Bay, and San Pablo Bay. The EMP is one of the nation’s oldest environmental monitoring programs and has compiled over four decades of consistent and comprehensive water quality and biological data.


  • 1971: Start of Environmental Monitoring Program Water Rights Decision 1379
  • 1978: Water Rights Decision 1485
  • 1983: Addition of continuous monitoring stations 
  • 1999: Water Rights Decision 1641
  • 1995: Integration with CDFW Zooplankton Monitoring
  • 2017: New Research Vessel Sentinel


Discrete Water Quality and Nutrients

Physical water quality parameters are measured using YSI EXO2 multi-parameter sonde with sensors for water temperature, dissolved oxygen, specific conductance, pH, turbidity, chlorophyll fluorescence.

Water for nutrient samples are collected at a depth of approximately 3 feet using a Van Dorn sampler (van stations), a submersible pump or a flow through system (vessel stations). Samples are analyzed by DWR’s Bryte Laboratory for chloride, chlorophyll a, pheophytin a, nitrate, nitrite, nitrogen, organic carbon, organic nitrogen, ortho-phosphate, phosphorus, silica, total/dissolved solids, and total/volatile suspended solids.

Set up of EMP nutrient and chlorophyll a sample processing.
Set up of EMP nutrient and chlorophyll a sample processing. CDWR image.
Map showing the current discrete water quality monitoring stations for EMP.
Map of the current EMP Discrete Water Quality Stations. CDWR image.
(click to enlarge in new window)


Phytoplankton samples are collected alongside discrete nutrient samples with a submersible pump from a water depth of one meter (approximately three feet) below the water surface. Samples are stored in 50-milliliter glass bottles with 2mL of Lugols solution to act as a stain and preservative. Currently, phytoplankton samples are analyzed by BSA Environmental, Inc.  Phytoplankton are identified to the lowest taxonomic level possible using the Utermöhl method and APHA standard methods (Utermöhl 1958, APHA 1998).

Woman standing inside the cabinet of boat in front of a window pouring a water sample through a filtration device for processing phytoplankton samples.
EMP Staff processing water samples. CDWR image.
Map showing the current phytoplankton monitoring stations for EMP - link opens in new window.
Map of the current EMP Phytoplankton monitoring stations. CDWR image.
(click to enlarge in new window)


The project uses three types of sampling gear: a mysid net (505 um mesh), a Clarke-Bumpus net (160 um mesh, targets adult and juvenile copepods, and cladocerans), and a pump (43 um mesh, targets adult and juvenile cyclopoid copepods of the genera Limnoithona and Oithona, copepod nauplii, and rotifers). The zooplankton tows are conducted obliquely through the water column for 10 minutes. A total of 19.8 gallons of water are sampled vertically through the water column for the pump samples. All samples are preserved in 10% formalin with Rose Bengal dye to aid in laboratory processing.

Fact sheets on how zooplankton can be incorporated into resource management.

Woman on a boat leaning over the rail grabbing a suspended metal frame with an attached conical shaped net that is used for capturing zooplankton.
Mysid and Clarke-Bumpus nets. CDWR image.
Map showing the current zooplankton monitoring stations for EMP - link opens in new window.
Map of the current EMP Zooplankton Monitoring Stations. CDWR image.
(click to enlarge in new window)


A Hydraulic winch and Ponar dredge are used to collect four replicate grabs at each of the ten benthic stations. The contents of each grab sample are washed over Standard No. 30 stainless steel mesh screen and carefully washed with a fine spray to remove as much of the substrate as possible. All material remaining on the screen after washing is preserved in a solution of approximately 10% buffered formaldehyde containing Rose Bengal dye for laboratory analysis, followed by transfer to 70% ethanol for long-term storage. An additional Ponar grab sample is taken and 500 ml of sediment is collected for analysis at the DWR Soils Laboratory.

Woman standing on the deck of boat grabbing the ponar dredge so contents can be dumped into a sampling bucket
Collecting a grab sample. CDWR image.
Map showing the current benthic monitoring stations for EMP - link opens in new window.
Map of the current EMP Benthic Monitoring Stations. CDWR image.
(click to enlarge in new window)

Relevant Reports

Obtain IEP Newsletter reports by sending email to iep@wildlife.ca.gov

  • IEP Newsletter Vol. 30, Issue 3, 2017
  • IEP Newsletter Vol. 29, Issue 2, 2016
  • IEP Newsletter Vol. 26, Issue 4, 2014

Related Information

Article: How Sheds Help Ensure Healthy Water Quality for Millions of Californians

Principal Investigator

Ted Flynn, Theodore.Flynn@water.ca.gov
California Department of Water Resources

Program Staff

Benthic Lead - Elizabeth Wells

Phytoplankton Lead -Tiffany Brown

Discrete Water Quality Leads
Sarah Perry, Sarah.Perry@water.ca.gov 
Julianna Manning, Julianna.Manning@water.ca.gov

Zooplankton Lead - Arthur Barros

Looking for Data?

Discrete Water Quality:
Sarah Perry, Sarah.Perry@water.ca.gov

Tiffany Brown, Tiffany.Brown@water.ca.gov

Arthur Barros, Arthur.Barros@wildlife.ca.gov

Elizabeth (Betsy) Wells, Elizabeth.Wells@water.ca.gov