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Discrete Benthics Meta Data – Elizabeth (Betsy) Wells
IEP Environmental Monitoring Program
Benthos Metadat

Last updated: Tuesday, July 22, 2015
I. Contact Information

Program Manager: Shaun Philippart

Lead Contact: Elizabeth (Betsy) Wells
Department of Water Resources
Division of Environmental Services
3500 Industrial Blvd., West Sacramento, CA 95691
(916) 376-9821

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 and San Pablo Bays. These objectives are met by establishing standards mandated in water right permits issued to the Department of Water Resources and U.S. Bureau of Reclamation 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 State Water Resources Control Board (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). 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 the SWRCB discussing data collected.

The benthic monitoring program is one element of DWR’s and USBR’s Environmental Monitoring Program (EMP) conducted under the Interagency Ecological Program (IEP) umbrella. The EMP also includes monitoring of water quality, zooplankton and phytoplankton. The overall objective of the benthic monitoring program is to determine the impacts of water project operations on the estuary. These impacts are interpreted by changes in benthic fauna presence, abundance and distribution associated physical factors in the estuary. Data collected from the benthic monitoring program is also used to detect newly introduced species in the estuary. To date, 436 species in ten phyla (Cnidaria, Platyhelminthes, Nemertea, Nematoda, Annelida, Arthropoda, Mollusca, Chordata, Phoronida and Echinodermata) have been collected from the study area. Sediment composition data are also collected as part of the benthic monitoring program to document general trends in sediment composition for all sites where benthic samples are collected.

III. Study Area and Sample Sites

A. General Information

Geographic coverage of the sampling sites ranges from San Pablo Bay east through the upper Estuary to the mouths of the Sacramento, Mokelumne and San Joaquin rivers. The study area currently comprises ten sites that are sampled monthly. These sites represent a wide variety of habitats that vary in size and physical make-up as well as water quality and sediment composition. The aquatic habitats sampled range from narrow, freshwater channels in the Delta to broad, estuarine bays. The mixing of river water with tidal water creates a wide range of water quality conditions. For example, salinity ranges from freshwater to around 29 ppt in the most western sites.

B. Name and Location Information for Benthos Sampling Sites


  • Coordinates are in decimal degrees
  • Channel position is determined while facing downstream.
IV. Period of Record

Benthic monitoring began in 1975. From 1975 through 1979 the program collected samples biannually from 18 to 35 stations, for a total of 48 stations over the period. In reviewing data collected between 1975 and 1979, it became evident that semi annual monitoring was insufficient to reveal long term ecological changes as mandated by Water Right Decision 1485. In 1980, DWR revised the benthic monitoring program and began monthly sampling at nine stations. In 1995, major program revisions were implemented to the program. A review of the data collected from 1980 to 1990 recommended that across-channel sampling be reduced to a single station per location in the Delta so that the geographic coverage could be widened. These revisions included increasing the number of sites sampled each month from nine to ten and increasing the number of grab sample replicates from three to four. Detailed information about location, number and characteristics of the historical sites can be found in IEP Technical Report 12 (Markmann, 1986) and IEP Technical Report 38 (Hymanson, et al., 1994).

A programmatic review of the EMP in 2001-2002 found that the benthos monitoring element was particularly in need of fundamental and comprehensive consideration through intense special studies and study design examination. Reviewers recommended a temporary reduction in sampling frequency to free up EMP resources to conduct the more spatially intense sampling without requiring additional resources. October 2003 was the last of the monthly sampling events and sampling continued quarterly (in October, January, April, July) at the stations sampled through October 2005 when monthly sampling resumed.

V. Sampling Frequency

Biannual sampling was conducted in late spring and fall, from 1975 to 1979. Monthly sampling started in June 1980 and ended in October 2003. Samples were collected quarterly from October 2003 through October 2005. Currently samples are collected monthly.

VI. Data availability in EMP's benthic database

A. Sampling events

B. Grabs

VII. Field Collection Methods

A. Benthos

All samples are collected using a hydraulic winch and Ponar dredge. The Ponar dredge samples a bottom area of about 0.052 m2 to a depth that varies with the type of sediment and the ability of the dredge to penetrate it. Under the current program four replicate sample grabs are collected at each sampling site. The contents of the dredge are brought to the surface and placed in a large plastic bucket. Water is then added to the sample to create slurry. The contents of each grab sample bucket are washed over Standard No. 30 stainless steel mesh screen (0.595 mm openings). Each sample is 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 20% buffered formaldehyde containing Rose Bengal dye for laboratory analysis.

The benthic macroinvertebrate sampling methodology used in this program is described in Standard Methods for the Examination of Water and Wastewater, 20th ed. 1998 American Public Health Association, Washington D.C. (See pages 10-60 through 10-74.)

B. Sediment

Sediment samples are also collected as part of the benthic monitoring program. Samples are collected using the same hydraulic winch and Ponar dredge as the infaunal sampling. A single sediment grab is taken at each sampling site. The contents of the Ponar dredge are emptied into a plastic tub and a random subsample is placed into a 1-liter plastic jar for storage and transport to the DWR Soils Laboratory for analysis.

VIII. Lab Processing Methods

A. Benthos

At the laboratory, the volume of settleable substrate in each sample jar is estimated and recorded. The formalin fixative is poured off and the sample is thoroughly washed on a 30-mesh (0.6 mm) screen. The composition of the substrate is estimated and recorded noting the relative percentages of peat, sand, mica, organic detritus, and other materials. The substrate is hand picked for organisms under a three diopter illuminated magnifier.

Organisms are placed in 70% ethyl alcohol for subsequent identification. A stereoscopic dissecting microscope (70-120x) is used to identify most organisms. When taxonomic features are too small for identification under the dissecting scope, the organism is permanently mounted on a slide and examined under a compound microscope.

If more than four hours of picking is required, and a sample contains many organisms but few species, a one-fourth subsample is chosen at random. The subsample is picked and the results are multiplied by four to represent the total sample. The remainder of the sample is inspected to make sure no other taxa were overlooked.

Laboratory identification and enumeration of macro-benthic organisms in each sample is performed under contract by Hydrozoology Laboratory, P.O. Box 682 Newcastle, CA 95658. Analysis has been done by Hydrozoology for the program's entire period of record.

The list of all species of macro-benthic organisms identified and the total number of individuals counted can be found in the Benthic Dictionary. In the dictionary, the "Total counted" column is the total number or individuals counted since the beginning of the program; the "Reference" columns refer to the list of taxonomic references.

B. Sediment

All sediment samples are analyzed by the DWR Soils Laboratory, West Sacramento, CA. Analysis of a sediment sample involves determining the percent size fractions with the use of a mechanical sieve. The sieves sizes are as follow: 75, 37.5, 19, 9.5, 4.75, 2.36, 1.18, 0.6, 0.3, 0.15, 0.075, 0.005, 0.002, 0.001 mm. All particle sizes are found on a regular basis in the samples with the exception of gravel (particles greater than 4.76 mm in diameter).

The percent organic content of each sediment sample is also determined from the loss in weight of an oven-dried sample burned at 440 degrees Celsius for 8 hours. All laboratory analysis procedures follow the American Society for Testing Methods, D-2974, "Moisture, Ash, and Organic Matter "and D-422-63, "Particle-Size Analysis of Soil".

IX. Data Management and Summarization

A. Benthos

Identification and enumeration data is recorded onto datasheets by Hydrozoology Laboratory. These data are then entered monthly by DWR Personnel into EMP's Benthic database. After reviewing the results for accuracy and completeness, data are uploaded onto the BDMA webpage.

Data is in .csv file format, and available on a yearly basis with the current year available month by month. The fields available in the .csv file include:

  • Sample Date – Date sample was taken
  • Station – IEP station ID
  • Location – Description of station location, see also Currently Sampled Stations or Historically Sampled Stations
  • Grab # Identifies individual replicate grabs in a sample, set to 0 for missing samples
  • Organism code-Serial code used to identify a particular organism
  • Common name
  • Phylum – Organism information, see also Benthic Dictionary
  • Class – Organism information, see also Benthic Dictionary
  • Order – Organism information, see also Benthic Dictionary
  • Family – Organism information, see also Benthic Dictionary
  • Genus – Organism information, see also Benthic Dictionary
  • Species – Organism information, see also Benthic Dictionary
  • Count – Count of individuals found in the grab, a count of 0 identifies successful but empty grabs, see also lab processing methods
  • Subsample size – Factor by which sample was divided to reduce counting time, see also lab processing methods
  • Comments – Comments about the grab: sample lost, sample in poor condition, presence of vegetation, etc

Counts of individuals per grab can be expanded to abundance per unit area by averaging the individual species counts over the number of replicate grabs and multiplying by a constant (k) to obtain a number of individuals per m2 for a given sampling event. The value of k is computed as follows: k = 1 / sample area of the ponar dredge in m2.  The Ponar used by the EMP for benthic monitoring samples a bottom area of 0.052 m2.  Thus, the value of k for the EMP benthic data is 19.  

Note on lost & empty grabs: To correctly expand counts of individuals per grab to abundance per unit area, the data user must be careful to distinguish between a) scheduled sampling events that were missed entirely, b) grabs that were acquired in the field but were lost or were unusable for lack of correct preservation and c) grabs that, although successfully acquired in the field and correctly preserved, did not contain any macro-invertebrate organisms. These 3 cases are distinguished in the benthic database as follows:

  • Missing sampling events are entered with the target sampling date and station but with a single grab number set to zero. There is no species count data attached to these sampling events.
  • Lost and damaged grab samples are entered with their actual grab number in the replicate series and are marked with a comment such as "No data: sample lost". There is no species count data attached to theses grabs.
  • Grabs devoid of macro-invertebrates are entered with their actual grab number in the replicate series. These empty grabs have species data attached to them: a single pseudo species coded "None None None None" and a count of 0. They should be included in the average count calculation to ensure that abundance per unit area is computed reliably.

B. Sediment

Sediment composition data is provided to the program by the DWR Soils Laboratory in the form of monthly written reports. These data are then entered monthly by DWR Personnel into EMP’s benthic database.  For more information regarding the sediment data please contact Heather Fuller.

X. Reference

A. Taxonomic References

The list of taxonomic references contains all references used for species identification. The "Reference Code" column in this list is used in the "Reference" columns in the Benthic Dictionary to establish species-reference relationships.

B. Program Reports, Publications, and Other Pertinent Literature.

  1. California Department of Water Resources. 1975-1995. Annual Reports, Fiscal Years 1975-1995, Water Quality Conditions in the Sacramento-San Joaquin Delta. Sacramento, California. Sacramento (CA): California Department of Water Resources. Reports prepared for the State Water Resources Control Board.
  2. California Department of Water Resources. 1995. Sacramento-San Joaquin Delta Atlas. State of California, Department of Water Resources, Sacramento, California. 121 pp.
  3. Carlton, J.T., J.K. Thompson, L.E. Schemel, and F.H. Nichols. 1990. Remarkable invasion of San Francisco Bay (California, USA) by the Asian clam Potamocorbula amurensis. I. Introduction and dispersal. Marine Ecology Progress Series 66: 81-94.
  4. Dietel, C.1991. Asian clam invades San Francisco Bay. Outdoor California 52(5) 1-4.
  5. Fields, W. and C. Messer. 1999. Life on the Bottom: Trends in Species Composition of the IEP-DWR Benthic Monitoring Program. IEP Newsletter, Fall 1999. 12(4): 38-41.
  6. Herbold, B. and P.B. Moyle. 1989. The Ecology of the Sacramento-San Joaquin Delta: A Community Profile. Report prepared for the U.S. Department of the Interior, Fish and Wildlife Service. Biological Report 85(7.22). 107 pp.
  7. Hollibaugh, J. T. and I. Werner. 1991. Potamocorbula amurensis: Comparison Of Clearance Rates and Assimilation Efficiencies for Phytoplankton and Bacterioplankton. IEP Technical Report 29. 42 pp.
  8. Hymanson, Z., D. Mayer and J. Steinbeck. 1994. Long-Term Trends in Benthos Abundance and Persistence in the Upper Sacramento-San Joaquin Estuary, Summary Report: 1980-1990. IEP Technical Report 38. 68 pp.
    Download a scannned version of this report and its appendices.
  9. Hymanson, Z.P.. 1991. Results of a Spatially Intensive Survey for Potamocorbulaamurensis in the Upper San Francisco Bay Estuary. IEP Technical Report 30. 21 pp.
  10. Lehman, P. 1996. Water Quality Conditions in the Sacramento-San Joaquin Delta, 1970-1993. Report to the State Water Resources Control Board.
  11. Markmann, C. 1986. Benthic Monitoring in the Sacramento-San Joaquin Delta. Results from 1975 through 1981. IEP Technical Report 12. 51 pp. Out of Print. Download a scanned version of this report.
  12. Messer, C., G. Marsh and H. Peterson. 1999. Potamocorbula amurensis. IEP Newsletter, Spring 1999. 12(2): 22-23.
  13. Nichols, F.H. 1990. Invasion of San Francisco Bay by Potamocorbula amurensis- A Major Perturbation? Interagency Ecological Study Program for the Sacramento-San Joaquin Estuary Newsletter. June 1990. pp. 1-2.
  14. Nichols, F.H. and M.M. Pamatmat. 1988. The Ecology of the Soft-Bottom Benthos of San Francisco Bay: A Community Profile. Report prepared for the U.S. Department of the Interior, Fish and Wildlife Service. Biological Report 85(7.19). 73 pp.
  15. Nichols, F.H., J.K. Thompson, and L.E. Schemel. 1990. Remarkable invasion of San Francisco Bay (California, USA) by the Asian clam Potamocorbula amurensis: II. Displacement of a former community. Marine Ecology Progress Series 66: 95-101.
  16. Peterson, H. 1997. Clam-Stuffed Sturgeon. IEP Newsletter, Winter 1997. 10 (1): 21.
  17. Peterson, H. 1997. Potamocorbula amurensis. IEP Newsletter, Spring 1997. 10(2): 24.
  18. Stanford Research Institute. 1971. An Bay-Delta Monitoring and Analysis Section for the Sacramento-San Joaquin Delta and Suisun Bay. Report prepared for the State Water Resources Control Board. SWRCB Publication Number 40. 106 pp.
  19. State Water Resources Control Board. 1999. Water Right Decision 1641. 211 pp.
  20. Thompson, B. and H. Peterson. 1998. Benthic Macrofaunal Assemblages of San Francisco Bay and Delta. IEP Newsletter, Spring 1998. 11(2): 26-32.
  21. Tokita, J. 1994. The Delta Invaders. DWR News: The Coastal Branch Working with Nature. Spring 1994. Sacramento (CA): California Department of Water Resources. pp. 23-28.
  22. Vayssières, M and H. Peterson. 2003. Cross-channel Variability in Benthic Habitat. IEP Newsletter, Spring 2003. 16(2): 51-56.