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Discrete Water Quality Meta Data - Jenna Rinde
IEP Bay-Delta Monitoring and Analysis Section
Discrete Water Quality Metadata

Last updated: March 14, 2013
I. Contact Information

Program Manager: Shaun Philippart

Lead Contact: Shaun Philippart
Department of Water Resources
Division of Environmental Services
3500 Industrial Blvd, West Sacramento, CA 95691
(916) 375-4825
email Shaun Philippart

DWR Bryte Laboratory
1450 Riverbank Road
West Sacramento, CA 95605
(916) 375-6008

Sid Fong - Acting Supervisor Chem. Test Section
email Sid Fong

II. Study Mandate and Objectives

The State Water Resources Control Board (SWRCB) sets water quality objectives to protect beneficial uses of water in the Sacramento-San Joaquin Delta and Suisun Bay. These objectives are met by establishing standards mandated in water right permits issued to the Department of Water Resources (DWR) and U.S. Bureau of Reclamation (USBR) by the SWRCB. The standards include minimum Delta outflows, limits to Delta water export by the State Water Project (SWP) and the Central Valley Project (CVP), and maximum allowable salinity levels.

In 1971, the SWRCB established Water Right Decision 1379 (D-1379). This Decision contained new water quality requirements for the San Francisco Bay-Delta Estuary. D-1379 was also the first water right decision to provide terms and conditions for a comprehensive monitoring program to routinely determine water quality conditions and changes in environmental conditions within the estuary. The monitoring program described in D-1379 was developed by the Stanford Research Institute through a contract with the SWRCB. Implementation of the monitoring program began in 1972, as SWRCB, DWR, and USBR met to define their individual responsibilities for various elements of the monitoring program. In 1978, amendments to water quality standards were implemented and resulted in Water Right Decision 1485 (D-1485). More recently these standards were again amended under the 1995 Water Quality Control Plan and Water Right Decision 1641 (D-1641) established in 1999. The SWP and CVP are currently operated to comply with the monitoring and reporting requirements described in D-1641. D-1641 requires DWR and USBR to conduct a comprehensive environmental monitoring program to determine compliance with the water quality standards and also to submit an annual report to SWRCB discussing data collected.

Discrete water quality monitoring is one element of the Bay-Delta Monitoring and Analysis Section (BDMA) conducted by DWR and USBR with assistance from DFG and the USGS under the Interagency Ecological Program (IEP) umbrella. The BDMA also monitors water quality with a set of continuously recording automated stations, and it has complementary phytoplankton, zooplankton and benthic macro-invertebrates monitoring elements. The overall objective of the water quality monitoring program is to provide information for water resource management in compliance with flow-related water quality standards set forth in the series of Water Right Decisions described above. These decisions permit the USBR and DWR to appropriate water for operation of the CVP and the SWP. In return, the two agencies are required to monitor the effects of diversions and flow manipulations resulting from project operations and ensure the compliance with existing water quality standards. Another objective of the BDMA water quality monitoring is to provide abiotic information relevant to the interpretation of the results of the biological monitoring elements.

III. Study Area and Sample Sites

A. General Information

The study area includes the Delta within its legal boundaries, Suisun Bay and Suisun Marsh, and northeastern San Pablo Bay bounded by a line between Pinole Point on the east and the Solano County line on the north shore. The EMP sampling sites range from San Pablo Bay east through the upper Estuary to the mouths of the Sacramento, Mokelumne, and San Joaquin rivers. These sites represent the main inflows and outflows of the Sacramento-San Joaquin Delta, and Suisun Bay and Suisun Marsh. Currently, 19 sites are sampled monthly throughout the year and three sites are sampled monthly during certain seasons.

B. Name and Location Information for Discrete Water Quality Sampling Sites

  • Coordinates are in decimal degrees, Geographic coordinate system, North American Datum 1983 and have been verified to be accurate for 1:24,000 scale mapping.
  • Habitat types are based on ecologically important physical and chemical habitat characteristics.
  • Regions are based on cluster analyses of monthly water quality variables. For specific analyses see Lehman 1996 and Lehman and Smith 1991; Jassby and Cloern 2000;

C. Sample Sites' History and Rationale for Monitoring


  • "Rationale-1970" is from the Stanford Research Institute report to the State Water Resources Control Board of 1970.
  • "Rationale-2002" is from the EMP Review of 2001-2002.

IV. Period of Record

Most stations and variables monitored by the EMP were established based on recommendations by a 1970 Stanford Research Institute (SRI) study commissioned by SWRCB, or derived from the preceding "Delta-Suisun Bay Surveillance Program" and the "Delta Fish and Wildlife protection study." The original set of stations included both continuous recorders for salinity and temperature at shore stations and discrete sampling sites reached by boat or by road. The original number of discrete stations was expanded in 1978 to accommodate compliance monitoring for new water quality standards. In 1995, the number of stations was reduced to streamline monitoring efforts in the face of budgetary constraints and to free up funds for more special studies within the IEP. With the exception of one continuous multi-variable shore station (Sacramento River at Hood) and two entrapment zone stations (with variable location depending on bottom specific conductivity values), no completely new stations have been added throughout the program. Some sampling stations were moved to a nearby location over time to alleviate access problems or to shift from shore sampling to vessel sampling (or vice versa). In the EMP data base, all moved stations are identified by a modified station name (usually the letter A is added). However, the original station names are generally retained in the successive water right decisions specifying monitoring requirements for the EMP.

Similar to the sampling stations, most variables measured today are among the original variables measured in 1970. The most substantial changes occurred relatively recently with the addition of a continuous monitoring network recording multiple variables starting in 1983 (see shore-based continuous monitoring metadata), on-board recording of horizontal and vertical profiles of several constituents (see vessel-based continuous monitoring metadata), and the discontinuation of 15 discrete sampling sites starting in 1996. Heavy metal and pesticides monitoring was conducted twice a year from 1971 to 1995 and then discontinued. Zooplankton sampling was part of the original 1970 monitoring program, but then became a separate program until it was re-integrated in 1996. Water quality field measurements and chlorophyll a samples are taken at all the zooplankton monitoring stations although the complete set of water quality laboratory analyses is not

V. Sampling Frequency

From 1975 to 1994 water samples were acquired monthly in the rainy season (October or November to February or March) and bimonthly in the dry season (from March or April to September or October); with the following exceptions: 1983 monthly sampling all year, 1984 bimonthly in July to September; 1986 and 1994 bimonthly from June to September, 1993 bimonthly in July. Some constituents were sampled less often: metals and pesticides were sampled twice a year in May and September. Since 1995, samples are acquired monthly, with the exception of three stations (NZ002, NZ004, NZ325) that are sampled only when the surface specific conductivity is below 20,000 �S/cm.

Since 1975, the sampling times were planned to occur within a one hour window of the expected occurrence of high tide slack at the sampling location.

VI. Data availability in EMP’s Discrete Water Quality database

Although water quality data have been collected for some stations since 1968 under various programs, only data gathered by the EMP since 1975 are available here.

VII. Field Methods

Since 1975, off-shore sites were accessed with DWR and USBR research vessels equipped with the same instruments and sample handling facilities so as to be interchangeable. Most often monitoring cruises were conducted with the DWR-owned RV San Carlos, and the USBR RV Compliance (and since 2004, the RV Endeavor) was used when the San Carlos was not available. A lab van has been used for accessing sites sampled from a pier or bridge, currently only two sites (C3 and C10) are sampled with the lab van. Van sampling is a little less comprehensive than boat sampling, in particular horizontal and vertical profiles of some constituents are not recorded.

A. Field measurements

Calibration Procedures and Frequency: Procedures have been developed for routine testing, maintenance and calibration of the field measurement equipment. Instruments are calibrated to comply with manufacturers or laboratory specifications before and after the sampling run. Accuracy: The maximum deviation allowed for instrument calibration is 3 percent. If a post-calibration indicates significant drift has occurred during the run, data collected during the run are flagged as questionable. An "Instrument Maintenance, Calibration and Repair" log is maintained for each instrument documenting its condition, scheduled periodic services, the date, and the individual performing the calibration.

Vertical and horizontal profiles are also conducted monthly at all zooplankton tow sites for the following constituents: water temperature, dissolved oxygen concentration, specific conductance, turbidity, and chlorophyll a in vivo fluorescence. An Instrument Comparison Data sheet has been developed to help ensure validation of the continuous monitoring equipment by comparing results to those obtained with other on board devices.

B. Sample Collection

Samples are generally collected without duplication except when specified by a monthly rotational schedule for quality control purposes. Currently, one chlorophyll sample per day is duplicated, on a rotating basis, and one chemical sample per day is increased in volume (one quart rather than a pint) for QA/QC testing at the lab.

Water 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). Historically, supplemental samples were periodically taken 3 feet above the bottom. Pumps equipped with plastic impellers were used when necessary to avoid metal ion contamination. Pesticides samples were collected 1 foot below the water surface in glass bottles immersed directly into the water.

C. Sample Containers and holding times

The DWR Bryte laboratory supplies all necessary sampling materials to the EMP field sampling crews. Requirements for sample containers, preservation techniques, and holding times are found in one of the following references (or later editions): Standard Methods for the Examination of Water and Waste Water, American Public Health Association, et al., 19th Edition; Handbook for Sampling and Sample Preservation of Water and Wastewater, EPA 600/4-82-029, September 1982.

To monitor possible contamination during the collection, transport, and storage of water samples, two field blanks are taken each month (one in the lab van and one in the research vessel lab). Laboratory prepared blank water is processed in the same manner as regular samples including field filtration, addition of preservatives and storage.

VIII. Laboratory Methods

Since 1975, all water quality analyses are conducted by staff at the DWR Bryte Laboratory. Located in West Sacramento, its primary function is to analyze drinking water, surface water, groundwater, and wastewater. DWR Bryte lab has maintained certification by the Environmental Protection Agency and the California Department of Health Services for water analysis since 1978. It also provides quality assurance, and related technical services.

IX. Data Management

Field measurements are recorded on field data sheets and entered in the field module of DWR Bryte lab’s Field and Laboratory Information Management System (FLIMS) database on location. The field results are then loaded into EMP's Discrete Water Quality database and into Bryte lab’s database. Laboratory analyses are performed by DWR Bryte Laboratory and the results are entered in the FLIMS database at the lab. On a regular basis data from the FLIMS database are loaded into DWR’s Water Data Library (WDL) database. EMP’s laboratory results are retrieved from the WDL into EMP’s Discrete Water Quality database. After reviewing of the results for accuracy and completeness, EMP's discrete water quality data are available here.

X. Reference

A. Methodological Texts

  1. Bryte Chemical Laboratory Quality Assurance Manual. 2002. Quality Assurance Technical Document 8. Department of Water Resources Publications, Sacramento, California. 48 pp.
  2. Methods for Chemical Analyses of Water and Wastes. 1983. EPA-600/4-79-020
  3. Standard Methods for the Examination of Water and Wastewater. 1992. 19th Edition or later, APHA, American Water Works Association, Water Pollution Control Federation, Washington, D.C.
  4. Methods for Determination of Inorganic Substances in Water and Fluvial Sediments. 1985. Techniques of Water Resources Investigations, USGS, Book 5, Washington, D.C.
  5. Annual Book of American Society for Testing and Materials Standards. 1988. Volumes 11.01 and 11.02, ASTM, Philadelphia, Pennsylvania
  6. Official Methods of Analysis. 1994. 14th Edition, AOAC International, Arlington, Virginia
  7. Methods for Organic Chemical Analysis of Municipal and Industrial Wastes. 1982. EPA 600/4-82-057
  8. Guidelines Establishing Test Procedures for the Analysis of Pollutants Under Clean Water Act. 1984. Federal Register, EPA, 40 CFR, Part 136
  9. Biological Field and Laboratory Methods. 1973. EPA-670/4-73-001
  10. Test Methods for Evaluating Solid Wastes, Physical / Chemical Methods. 1986. EPA, SW846, Volumes 1A, 1B, 1C and II

B. Reports, Publications and Other Pertinent Literature

  1. Jassby, A. D.; Cloern, J. E.. 2000. Organic matter sources and rehabilitation of the Sacramento-San Joaquin Delta (California, USA). Aquatic Conservation 10 (5): 323-352.
  2. Lehman P. W. and R. W. Smith. 1991. Environmental factors associated with phytoplankton succession for the Sacramento-San Joaquin Delta and Suisun Bay Estuary, California. Est. Coast. Shelf. Sci. 32:105-128.
  3. Lehman, P. W. 1996. Water quality conditions in the Sacramento-San Joaquin Delta, 1970-1993. Environmental Services Office, Department of Water Resources, 3251 S Street, Sacramento CA 95818.
  4. State Water Resources Control Board. 1970. An Bay-Delta Monitoring and Analysis Section for the Sacramento-San Joaquin Delta and Suisun Bay. Stanford Research Institute. SWRCB Publication No. 40
  5. Triboli, K., Mueller-Solger, A. and Vayssi�res, M. 2003. The Grind about Sonicated Chlorophyll (or: Did a Method Change in 1998 Affect EMP Chlorophyll Results?) IEP Newsletter, Winter 2003. 16 (4): 13.