Bibliography Background About KRIS

East Marin-Sonoma Info Links

The information below describes data, maps, photographs, and bibliographic references currently found in KRIS East Marin-Sonoma, as well as provides some detail about relevant data and studies not available in KRIS due to access or time constraints on integration. 

Rainfall Data

Rainfall data available in the KRIS East Marin-Sonoma project come from several sources. The largest source is the National Weather Service and the California Data Exchange Center (CDEC) database. CDEC is a network of State and Federal agencies that collect and share climate data over the Internet, with real time gauges at some locations. Much of the data on CDEC is collected by the California Department of Water Resources. The primary purpose of the cooperative project is to assess and monitor flood risk. 

For more information on this overall subject, see the Background page on Precipitation.


Flow Data and Studies

Flow data in the KRIS East Marin-Sonoma project come from the U.S. Geologic Survey (USGS).  Records of average daily flow are in cubic feet per second. Water years (WY) begin on October 1 of the prior calendar year. For example, the 1998 water year started on October 1, 1997. 

Low flows can limit salmonid production in streams of the East Marin-Sonoma area by reducing available habitat and exacerbating problems associated with water quality.  Due to a Mediterranean climate, small streams are prone to completely losing surface flow in summer.  Stream surveyors of Sonoma Creek compared permitted diversions with their observations of diversions in tributaries of Sonoma Creek in 1996.  These data were published as Appendices to the Sonoma Creek Enhancement Plan and are the only available data addressing the affects of low flows and flow diversions on salmonid streams in the East Marin-Sonoma area.  These data include records of pending and permitted water diversions by the State Water Resources Control Board Division of Water Rights (SWRCB) and field observations.  

For more information on this overall subject, see the Background page on Flow.


Aquatic Insect Data

Aquatic insect communities make excellent indicators of the health of aquatic ecosystems and are widely used as an index of water quality. The KRIS East Marin-Sonoma project contains information on aquatic insects produced by the Marin County Stormwater Pollution Prevention Program with assistance from the Sustainable Land Stewardship Institute (MCSPPP 2000). 

Studies were conducted in four Marin watersheds, Arroyo Corte Madera del Presidio, Corte Madera Creek, Miller Creek, and Novato Creek.  In each watershed, sampling stations were located in a range of possible stream environments.  Sites were sampled in September 1999, April 2000, and Spring 2002.  The methods used for aquatic insect sampling followed the California Stream Bioassessment Procedure (CSBP) for non-point source assessments developed by the California Department of Fish and Game.  The CSBP is a regional adaptation of the U.S. Environmental Protection Agency (U.S. EPA) Rapid Bioassessment Protocols (Barbour et al. 1999).  Physical habitat quality was also assessed for sampling reaches using the U.S. EPA Protocols which involve a score of 0-20.  A Physical Habitat Quality Table from the CSBP provides a description of how the habitats were ranked.

Several biological metrics of aquatic insect data are presented in KRIS East Marin-Sonoma.  EPT Taxa represents the number of Ephemeroptera (mayflies), Plecoptera (stoneflies) and Trichoptera (caddis flies) insect orders. The total number of all individual taxa present is also an indicator of aquatic health and is commonly termed the Taxonomic Richness.  Decreases in EPT Taxa or Richness indicate impairment.  Highly impaired streams are typically dominated by one species. The highest percentage of organisms represented by one talon is Percent Dominant Taxon, which increases with impairment.  The fourth index presented in KRIS, Total Index of Biological Integrity (IBI), is a summary of multiple measures of aquatic insect metrics based on a scoring method developed the California Department of Fish and Game (Harrington et al., 1999).  Harrington describes the development and standards associated with the Russian River Index of Biological Integrity (RRIBI) as well as the scoring criteria. This method was developed with data on first to third order Russian River tributaries. The scoring criteria provide a means of interpreting relative impairment using the results for particular metrics as well as a precursor to IBI. The reference values on KRIS Charts for aquatic insect data delineate "highly impaired" conditions according to these criteria.

The MCSTPPP report noted that use of the RRIBI for regional comparison should be appropriate due to the relative proximity of Marin County streams to the Russian River.  However, the RRIBI was intended for use in first to third order streams and may be of limited use in the lower-most sites of the Marin streams.  In addition, the RRIBI was a demonstration project and scoring methods are continuing to develop to be made more appropriate for other watersheds.  

For more information on this overall subject, including the CSBP and the RRIBI, see the Background page on Aquatic Insects.

The Bay Area Stream Fishes Database

Rob A. Leidy of the Environmental Protection Agency sampled fishes in over a hundred stream locations in the San Francisco Bay area during the years 1992-1998. All of the 31 sites in Marin County and the 32 sites in Sonoma County were sampled using multiple pass electrofishing, block nets and sites of a minimum 30 meters in length. The San Francisco Estuary Institute (SFEI) integrated the Leidy data into a relational database, produced a map of locations and produced a document presenting metadata and an electronic version of datasheets for individual locations. This document (SFEI 1999) provides details on how the data was collected and provides the basis for constraints on use of the data as adhered to in KRIS East Marin-Sonoma. Charts in KRIS present indices describing native fish composition and salmonid abundance. Data tables provide additional information describing site locations such as Site IDs which can be used to locate sampling sites on the Map provided.

For more general information on this overall subject, see the Background page on Fish Populations.

Fisheries and Habitat Data by A.A. Rich and Associates

A.A. Rich and Associates have been contracted to perform fisheries studies for four watersheds in the KRIS East Marin-Sonoma Project Area: Corte Madera Creek, Arroyo Corte Madera Creek, Novato Creek, and Adobe Creek (Petaluma Creek Tributary). All studies involved habitat classification by methods based on Bisson et al. (1982) and electrofishing. Habitat descriptions and fisheries sampling intensity varied among studies. Moreover, electronic data was not provided by Alice Rich, and available data was limited to reports for each of the four studies. From these reports, all data describing fish density, fish community structure, and standard habitat parameters were charted in KRIS East Marin-Sonoma.  In some cases appendices on fish stocking or local spawning surveys were also used as sources for data.

The A.A. Rich study of Arroyo Corte Madera del Presidio Watershed (1995) sought to evaluate the feasibility of stream rehabilitation by surveying habitat conditions, sample fish communities, and describe potential restoration projects.  This work was done for the Mill Valley Stream Keepers. Habitat typing was conducted for Old Mill Creek only which was deemed the most "natural" of streams in the watershed. This habitat data reveals shallow pools and an absence of spawning gravels except in Old Mill Park and above Three Wells which may be inaccessible to steelhead. Water temperatures ranged from 8.3-13.7C. A.A. Rich concluded that the limiting factor for fish abundance and diversity was a lack of water, and that poor habitat conditions were exacerbated by cement channels, particularly from Mill Valley downstream.

Fisheries Resources of the Corte Madera Creek Watershed (2000) was prepared for the Friends of Corte Madera Creek Watershed.  This study involved extensive electrofishing and temperature recording and concluded that the primary factors limiting steelhead populations appeared to be lack of streamflow and simplified habitat as a result of altered streambanks.  Numerous unregistered diversions were observed in the stream.

Fishery Resource Conditions of Novato Creek (1997) was prepared as part of an Environmental Impact Report concerning the Novato Creek Flood Control Project and under contract with Marin Public Works.  This small study involved electrofishing and a summary of information available on trout populations in Novato Creek.

Fishery Resource Conditions of Adobe Creek (1999) was prepared as part of an Environmental Impact Report concerning Lafferty Ranch and under contract with the City of Petaluma. This small study involved electrofishing and a summary of information available on trout populations in Adobe Creek.

For more general information on these overall subjects, see the Background pages.


California Department of Fish and Game Fisheries Data 

The California Department of Fish and Game (CDFG) Region 3 sampled Corte Madera Creek using electrofishing in 1969.  These data were never published or prepared in a report, but provided for use in KRIS by Bill Cox of CDFG.  CDFG is also responsible for oversight of hatchery operations and planted of juvenile salmon and steelhead in the project area. 

 For more general information on this overall subject, see the Background page on Fish Populations.

Coho Presence and Absence Surveys

Direct observation and single pass electrofishing were used by Adams et al. (1999) to determine presence and absence of coho salmon relative to historic surveys throughout the Central California region (ESU), including Sonoma and Marin counties.  These data summarize coho absence rate by county and are based on data up to the year 1997. Because the varying returns of different year classes of coho, three consecutive years of survey are needed for definitive presence/absence information.  The California Dept. of Fish and Game has conducted subsequent surveys for the presence and absence of coho salmon in the region.  However, effort in the East Marin-Sonoma project area between 1997 and 2002 consists only of surveys of Corte Madera Creek in 1999 when no coho salmon were found.

For more general information on this overall subject, see the Background page on Fish Populations.

Miller Creek Fish Behavior Study by Humboldt State University 

Humboldt State University student Nick Simpson conducted a fish behavior study in five pools in a short reach of Miller Creek in August of 2002.  The purpose of the study was to examine interspecific and intraspecific fish schooling behavior, but the results are presented in KRIS to show the fish community structure in Miller Creek.

For more general information on this overall subject, see the Background page on Fish Populations.

Corte Madera Creek Resource Evaluation by the San Francisco Bay Regional Water Quality Control Board

The Corte Madera Watershed Resource Evaluation and Information Report (1994) is a draft prepared by staff of the San Francisco Bay Regional Water Quality Control Board and includes some data collected in the summer of 1993 and the February 1994.  The field work involved fish and macroinvertebrate sampling, habitat surveys, and some water quality sampling.  Electronic data was not available from this work except for temperature and dissolved oxygen single-sample measurements taken in Corte Madera Creek and its tributaries on February 13, 1993.  The report does provide, however, some quantitative summaries of canopy, streambank, and riparian condition as well as comprehensive description of what resources and studies have been completed for Corte Madera Creek.

For more general information on these overall subjects, see the Background pages.

Water Quality Monitoring

Water quality data available in KRIS East Marin-Sonoma comes from the California Department of Fish and Game (CDFG), Petaluma Tree Planters monitoring in the Petaluma River watershed, San Francisco Bay Regional Water Quality Control Board monitoring in the Corte Madera Creek watershed, and Sonoma County Water Agency monitoring in the Sonoma Creek watershed.

California Department of Fish and Game: As part of the Marin and Sonoma Counties Agricultural Runoff Influence Investigation (MSCARII), CDFG monitors water quality at sites in the Petaluma Creek watershed, as well as Americano Creek, Stemple Creek, and Lagunitas Creek watersheds, and along the eastern and southern shoreline of Tomales Bay.  The objective of this program is to determine agricultural impacts on water quality.  Water quality parameters are generally measured bi-weekly during the rainy season and include dissolved oxygen, conductivity, turbidity, pH, temperature, ammonia, and biological oxygen demand.  Sampling began at some of these sites during 1991 and the program is still active.  Results of this monitoring can be found in Rugg (2000 and 2002).  CDFG has also provided spatial data locating sampling sites and notes describing sampling conditions for individual sites and days.  

Petaluma Tree Planters: Diazinon and chlorphyifos were analyzed from dry weather and storm related samples collected in and around Petaluma during July through November 1998, using the enzyme-linked immunosorbant assay (ELISA) method.  The first event was collected to characterize dry base flows, the second event represented the first storm and characterized the "first flush," which often washes accumulated pollution into storm drains and water bodies, and the last two events represented subsequent storms.  Sampling stations were selected according to varying land uses.  These data are presented in Abelli-Amen, 1999.  The purpose of this study was to determine whether diazinon and chlorpyrifos occurred in the watershed at concentrations of concern.  These chemicals are commonly used insecticides that can be toxic to aquatic life at relatively low concentrations.  Studies have shown toxic concentrations in Bay Area urban creeks, however to this point no studies had been conducted in the upper Petaluma River watershed.  A Total Maximum Daily Load (TMDL) is now being developed by the San Francisco Bay Regional Water Quality Control Board (2002) for diazinon and pesticide related toxicity in Bay Area urban streams.  Currently Arroyo Corte Madera del Presidio, Corte Madera Creek, Coyote Creek, Gallinas Creek, Miller Creek, Novato Creek, Petaluma River, San Antonio Creek, and San Rafael Creek are listed as impaired waterbodies under 303(d) for diazinon (SWRCB, 2003).  

San Francisco Bay Regional Water Quality Control Board (SBFRWQCB): Water quality parameters were monitored as part of a larger effort which also included habitat, fish, and macroinvertebrate surveys in the Corte Madera Creek watershed during 1992 and 1993 and reported in Corte Madera Watershed Resource Evaluation and Information Report (1994) .  There are additional water quality monitoring data from the SFBRWQCB that are not available in this draft, but may be incorporated into subsequent versions of KRIS.  These include water samples cooperatively collected with the Department of Water Resources and the State Water Resources Control Board from the Petaluma River watershed during 1973-1978, 1982-1987, and 1993 and from the Sonoma Creek watershed during 1974-1988.  The water quality parameters analyzed primarily included nutrients, dissolved oxygen, temperature, and coliform bacteria.  These data can be accessed in the U.S. Environmental Protection Agency's STORET online database at

Sonoma County Water Agency (SCWA): SCWA monitors water quality in receiving waters of the Sonoma Valley Treatment Plant (SVTP) according to NPDES requirements.  Three other municipal wastewater treatment plants exist within the KRIS East Marin-Sonoma project area:  City of Petaluma, Novato Sanitation District, and Las Gallinas Sanitation District.  Of these, only the City of Petaluma discharges into stream or river systems above potential freshwater fish habitat and no data from that operation was available in time for this draft KRIS East Marin-Sonoma.  NPDES requirements specify monthly monitoring of water quality parameters during periods of discharge. The SVTP discharges during the wet months (November-May) into Schell Slough and stores treated wastewater in reservoirs during the dry months. Remaining storage is discharged into Hudeman Slough as needed beginning in November.  Water quality data from SVTP receiving water samples was not be completely captured in KRIS East Marin-Sonoma due to the disintegrated form of the data as maintained by SCWA. Furthermore, no summaries or metadata were available. For the purpose of cursory evaluation of this data collection program, a single topic showing dissolved oxygen measurements for 1997 was produced.

Additional water quality monitoring has been conducted in the KRIS East Marin-Sonoma area.  However this data was either not readily accessible or outside the scope of this project.  This includes the following monitoring efforts in the Petaluma River watershed.  The San Francisco Estuary Institute's Regional Monitoring Program for Trace Substances includes water quality monitoring at the mouth of the Petaluma River, along with many other Bay sites and can be accessed at  In addition, water quality has also been measured by the Sonoma and Marin County Farm Bureaus, Grant Elementary School, Casa Grande High School.

School groups have also measured water quality parameters in Arroyo Corte Madera del Presidio, Corte Madera Creek, Miller Creek, and Arroyo San Jose.  This data along, with school-based restoration information, was collected by the North Bay Riparian Station and can be found at  In addition, community leaders have been collecting water quality information since the 1970's in Novato Creek.  This data is currently being compiled by the Friends of Novato Creek.

References for water temperature on charts are derived from McCullough (1999), while those for other water quality parameters come from the SFBRWQCB Basin Plan (1995).  For more general information on this overall subject, see the Background pages on Water Quality.

Water Temperature Monitoring by Sonoma Ecology Center

The Sonoma Ecology Center (SEC) provided stream temperature data for numerous sites in the Sonoma Creek Watershed for the years 1996 through 2002.  The description of locations for monitoring sites can be viewed as a table.  SEC began monitoring water temperatures in the Sonoma Valley to collect baseline data on watershed conditions and to determine if summer water temperatures were limiting steelhead production.  The monitors were installed during the summer season, mid-July until late October. Monitoring sites were chosen at deep pool habitats (usually 2 to 3 feet deep), in shaded sections of the stream. SEC published their initial findings in a draft report, Water Temperature Monitoring, Sonoma Creek Watershed, 1996-1997.  Results indicated a need for a more comprehensive monitoring program, and in 1998, twelve monitoring sites were chosen in upper mainstem Sonoma Creek and several main tributaries, based on their potential to provide juvenile steelhead rearing habitat.  A 1998 Water Temperature Monitoring Report was produced separately.  In 1999 through 2002, seven sites were monitored.  Monitoring was conducted by the Sonoma Valley Watershed Station, part of the SEC.  A report for the 2002 stream temperature monitoring is due in spring, 2003.  

For more general information on this overall subject, see the Background pages on Water Quality.


Stream Habitat Surveys in Sonoma Creek Watershed

Habitat surveys in the Sonoma Creek Watershed were coordinated by the Southern Sonoma County Resource Conservation District with the cooperation of hundreds of private landowners.  Protocols followed the California Salmonid Restoration Manual (Flosi et al. 1998).  Training, technical review and report development were provided by Bob Coey, Bill Cox, and Ken Bunzell of the California Department of Fish and Game.  Surveys were conducted in 1996 in Sonoma Creek above  Madrone Road, Asbury Creek, Bear Creek, Calabazas Creek, Graham  Creek, and Stuart  Creek.  Additional streams in the Sonoma Creek watershed have been surveyed in 2001 and 2002 under the leadership of the SSCRCD and in association with the Sonoma Ecology Center.  The only data available from these surveys were that published in Appendices to the Sonoma Creek Enhancement Plan and limited upper Sonoma Creek.

These types of stream habitat surveys provide an inventory of stream conditions which is useful for assessing suitability for coho salmon and steelhead trout.  Of all data available from these surveys, four habitat attributes of particular importance (percent habitat type by length, maximum pool depth, embeddedness, and canopy) are charted for particular streams. The relative proportions of a stream falling under the simple habitat types of flatwater, riffle, and pools can be a useful indicator of fish habitat condition because coho salmon and 1+ steelhead require pool habitat for successful rearing. The deeper the pools the better and thus maximum pool depth is a useful measurement of habitat quality. Embeddedness from these surveys is used as a rough estimate of spawning gravel quality, although bulk gravel samples are far superior as a monitoring tool. Canopy measurements in habitat typing surveys are quantitative and give indications of opportunities for stream warming and long term prospects for large wood recruitment. In addition, shelter rating and residual pool volume have been charted. Shelter rating describes the complexity of habitat while residual pool volume is a measure of pool habitat quantity. 

The CDFG Restoration Manual is available at   For more general information on this overall subject, see the Background page on Habitat Typing.


Stream Habitat Surveys in Arroyo Corte Madera del Presidio Watershed

Kier Associates conducted salmonid habitat typing surveys in streams in the Arroyo Corte Madera del Presidio watershed during April 2003.  The survey crew followed California Department of Fish and Game habitat typing protocols as outlined in the California Salmonid Stream Habitat Restoration Manual (CDFG 1998).  The Arroyo Corte Madera del Presidio watershed covers approximately 6 square miles in eastern Marin County and extends southeast from the East Peak of Mount Tamalpais to Richardson Bay.

The Mill Valley StreamKeepers funded the survey with a grant from the Marin County Stormwater Pollution Prevention Program.  In 1994, A.A. Rich and Associates began a habitat survey, but it was never completed.

The survey on Arroyo Corte Madera del Presidio began at the Marin Theater Company (397 Miller Avenue) and stopped at the edge of incorporated land where the steep slope prevents fish passage.  Several tributaries were also surveyed.  Old Mill Creek was surveyed up to Cascade Dam.  Cascade Creek was surveyed to the waterfall (a natural migration barrier).  Warner Creek was surveyed to the man-made marsh located at the municipal golf course.  A survey was attempted on Sutton Manor Creek, but limited flow and a 0.25 mile concrete channel make it unsuitable for salmonids.  

The CDFG Restoration Manual is available at  For more general information on this overall subject, see the Background page on Habitat Typing.


Temperature Monitoring in Arroyo Corte Madera del Presidio Watershed

In conjunction with stream habitat surveys, Kier Associates collected stream temperature data using automated probes in four sites in the Arroyo Corte Madera watershed during May-October 2003. The sites are:
AC_01 = Arroyo Corte Madera del Presidio just below confluence of Warner Creek
AC_03 = Arroyo Corte Madera del Presidio just above Blithedale Park
AC_04 = Old Mill Creek just below Ethel Avenue
AC_05 = Old Mill Creek below Three Wells Park

For more general information on this overall subject, see the Water Quality Background page.


Geomorphic Assessment of Corte Madera Creek Watershed by Stetson Engineers, Inc. 

Stetson Engineers, Inc. investigated the geomorphic factors related to flood control within the watershed and published Geomorphic Assessment of the Corte Madera Creek Watershed (2000) with separate Appendices. The study estimated a preliminary bedload sediment budget and identified sediment sources within the watershed.  Stetson Engineers determined that sediment production in the Corte Madera Creek watershed was 'unnaturally' high and compared the results to the sediment yield data of other regional watersheds.  Information on land management, vegetative cover, geologic units and terrain, landslide distribution, and gully distribution were collected for the report and presented in a series of maps.  The study also presented conceptual designs for floodplain restoration and bank stabilization. 

Bedload sediment budget estimations were made using the SEDCOMP batch mode program with Parker-Klingeman (1982) procedures to estimate bedload sediment yield from ten major subwatersheds above the town of Ross.  Field data were collected in each subwatershed for model input.  These inputs included: cross-sections (historical data and 2000 data), Wolman pebble counts, and subsurface bulk samples.  Bulk subsurface samples were collected using Milhouse (1973) methods.  The surface and subsurface data were used to determine bed roughness values.  Both Parker-Klingeman and U. S. Forest Service shear values were used as inputs to the model to provide a range of estimated bedload yield.  Results of the sediment budget were assumed to be underestimated since the model did not include 'very fine' to 'fine' sands.  The uncalibrated model estimated that bed and bank erosion produced approximately 9 percent of the total bedload sediment yield and that fluvial transport from hillslopes generated 91 percent.  Human-induced bedload sediment was estimated to be approximately 1,600 tons/year. 

For more general information on this overall subject, see the Background page on Sediment.


Geomorphic Studies by Laurel Collins

Laurel Collins investigated geomorphic conditions in several watersheds within the KRIS East Marin-Sonoma project area. Novato Creek, Carriger Creek, and San Antonio Creek were each surveyed using similar methodologies. The primary objectives of the studies were to identify sediment sources and landscape processes affecting stream habitat conditions. Recommendations were made in each study for reducing identified sediment sources. In each survey, a centerline tape was pulled continuously along the channel and data were referenced to stations along the tape. Data collected included:

        ·        bank conditions - stable, revetted, and eroding (eroding is > 0.5’ avg bank retreat).

        ·      locations, size, and types of culverts and other engineered structures crossing the creek.

        ·        cross sections to establish bankfull width and terrace heights. 

        ·     visual estimates of D50 size classes on the bed surface.

        ·     volume of sediment generated by bed incision, taken by estimating incision within the last 165 years.

        ·     reconstructing the historical channel elevation and planform using visual estimates, air photos and          

              historical records.

        ·        pools and their characteristics, including causes of pool formation and pools spacing. 

        ·        woody debris number, spacing, species, and recruitment processes.

The general methodology is not standard, but parameters used in the studies are useful in characterizing salmonid habitat. Pool habitat, especially the number of pools and their depths, can be an important indicator of stream quality. Data on bank features can be used to characterize the quantity and quality of conditions. However, pool spacing and large woody debris spacing do not follow methods described in scientific literature and therefore cannot be compared to data collected from other streams. These studies refer to spacing as a linear distance between objects, whereas the standard definition of spacing in stream surveys is the ratio of the number of objects per reach per channel width.

In Novato Creek, the study reports that modern land uses in the upper watershed have increased sediment supply while tidal marsh reclamation has decreased downstream sediment transport. The result is an aggraded channel in the lower reaches of the stream. In addition, Stafford Dam has increased the drainage area by 5.2 square miles by connecting additional drainages in the upper watershed.

Findings from the Carriger Creek study show that portions of the lower mainstem channel have been severely altered from the destruction of distributary channels. Historically, Carriger Creek divided into at least three distributaries on its alluvial fan near Arnold Bridge. A review of 1946 air photos showed that portions of the northern and middle distributaries were plowed-over for agricultural purposes before the mid 1800’s. The study also suggests that the straightening of the channel upstream of the   Arnold  Bridge  for flood control contributed to degradation of salmonid habitat.

In San Antonio Creek, the study notes that this stream was a productive steelhead fishery until the mid 1900s. The draining of a small headwater wetland has increased the magnitude and frequency of peak flows while lowering the water table in the  Chileno Valley. The tidal channel of San Antonio Creek was also diverted from its natural tidal slough through the much smaller and shorter Schultz Slough around 1930. This alteration has flattened the gradient of the stream and contributed to aggradation in the lower reaches.   

For more general information on this overall subject, see the Background page on Sediment.


Sediment Yield Estimates for Sonoma Creek and Petaluma River Watersheds

The report, “PSIAC Model: Sediment Yields in Sub-watersheds of Sonoma Creek,” was prepared by Natural Resource Conservation Service (NRCS) AmeriCorps of Petaluma, California, in September, 1996.  It was published as a chapter in the Sonoma Creek Watershed Enhancement Plan, prepared by the Southern Sonoma County Resource Conservation District in June, 1997. The Pacific Southwest Inter-Agency Committee (PSIAC) model was developed in 1968 as a watershed assessment tool used to estimate sediment yield, the volume of sediment that reaches some arbitrary point in the watershed.  For this study, the authors chose the point where the stream gradient of Sonoma Creek levels out at the valley floor.  

Ten subwatersheds were evaluated for their potential to deliver sediment to Sonoma Creek.  Nine model factors (surface geology, soils, climate, runoff, topography, ground cover, land type, upland erosion and channel erosion/sediment transport) were assigned a rating based on empirical data using the PSIAC rating sheet.  Natural Resources Conservation Service TR-55 program was used to evaluate runoff values.  The rating factors were summed for each subwatershed and correlated to average annual sediment yield values in tons per acre. Hooker Creek contained the largest estimated sediment yield, with 1.74 tons per acre. Calabazas, Stuart, Agua Caliente, and Nathanson creeks had sediment yields between 1.29 and 1.44 tons per acre. 

For comparison, data from the U.S. Geological Survey for Sonoma Creek showed that suspended sediment yield at the USGS gage was 30,478 tons per year, while the PSIAC model estimated 29,100 tons per year.  However, the authors caution that the PSIAC model is best used to compare subwatershed sediment contributions and not as hard data. 

A survey of literature shows that refinements have been made to the PSIAC model in terms of its subjectivity (Johnson and Gebhart, 1982).  However, the Sonoma Creek study lacks proper references and cannot be evaluated for comparisons to other more recent PSIAC studies.

For more general information on this overall subject, see the Background page on Sediment.


Sediment Studies by Sonoma Ecology Center

The Sonoma Ecology Center prepared two reports on sediment in the Sonoma Creek Watershed.  The first, Spawning Gravel Suitability Assessment, Sonoma Creek Watershed, prepared by Mitchell Katzel and Oona McKnight in 2001, assessed spawning gravel quality at four locations in Sonoma Creek and at four in tributary streams.  According to the report, “The extent to which framework gravel sizes and fine sediment content may be adversely affecting spawning habitat and thereby limiting steelhead (and possibly Chinook salmon) populations in the Sonoma Creek watershed were investigated.”  During their field investigations in 1998, the authors used Wolman pebble count and McNeil dry bulk sampling methods at each study site to investigate the surface and subsurface gravel quality, respectively.  Surface particles showed no clear trend towards fining as the authors sampled upstream to downstream. Also, most of the surface samples fell within a mean bed particle size between 10 and 45 mm suitable for steelhead spawning gravel material (Kondolf, 2000).  None of the subsurface samples exceeded 30% particles less than 3.35 mm, or 14%  particles <1 mm, values noted significant to egg and alevin survival according to Kondolf.  The study concluded that neither erosion nor sediment production to stream channels in those portions of the Sonoma Creek watershed investigated was likely to be a significant factor affecting fish habitat, particularly spawning conditions.

The second report, Volunteer Monitoring of Suspended Sediment Concentration and Turbidity and Watershed Monitoring of Road Remediation in Annadel State Park, 2002,  prepared by Rebecca Lawton, Rich Hunter, and J. Menze of the Sonoma Ecology Center for the San Francisco Bay Regional Water Quality Control Board, analyzed stream monitoring data pertaining to road-related erosion in Annadel State Park (Annadel), near Santa Rosa, California.  Prior to the study, several degraded roadways were decommissioned, recontoured, or converted to narrow trails in the Sonoma Creek portion of Annadel. The remediation work sought to address sediment delivery to Sonoma Valley’s fish-bearing streams. According to the report, results of each portion of the project were as follows: 

For more general information on this overall subject, see the Background page.


Road and Trail Related Erosion

Data on roads in the KRIS East Marin-Sonoma project area are not completely mapped. Road data from the U.S. Geological Survey at the 1:100,000 and 1:24,000 scale may both be dated as only roads built at the time the USGS topographic maps were made currently show. Roads are a major source of sediment to streams. Surface erosion from roads can produce chronic sources of fine sediment which can diminish salmon and steelhead spawning success. Failure of roads during major storm events can lead to large landslides which can overwhelm streams with sediment, thus filling pools and diminishing habitat diversity. 

For more general information on this overall subject, see the Background page on roads.


Watershed, Stream, and Restoration Photographs and Maps

Photographs are presented in KRIS East Marin-Sonoma to shed light on current and historic watershed conditions, as well as to highlight monitoring efforts and restoration projects.  Pictures for the Arroyo Corte Madera del Presidio watershed were provided by The Bay Institute and Andy Peri, of the Mill Valley StreamKeepers.  The latter group of pictures represent photopoints at each reach where Peri and volunteers conducted habitat studies in 1996-1997.  Many pictures show volunteers holding a sign which marks the beginning of a reach.  While the photos and monitoring sites are captured in KRIS, the habitat data was not ready for publication.  The Bay Institute (TBI) provided photos of restoration projects coordinated by the Marin County Stormwater Pollution Prevention Program (MCSTOPPP), and The Students and Teachers Restoring A Watershed (STRAW) Project, which coordinates and sustains a network of teachers, students, community members, and restoration specialists as they plan and implement watershed studies and restoration projects in Marin and Sonoma counties.  STRAW provides teachers and students with the scientific, educational and technical resources to prepare them for hands-on, outdoor watershed studies, including ecological restoration of riparian corridors.  STRAW’s overarching goals are to empower students, support teachers, restore the environment and reconnect communities.  TBI has also provided photos from STRAW projects in the Miller Creek watershed. 

Sources of photos for the Corte Madera Creek watershed include Charles Kennard (Friends of Corte Madera Creek Watershed), A.A. Rich and Associates, and the U.S. Army Corps of Engineers.  Charles Kennard's images represent a cooperative restoration project on Sleepy Hollow Creek at Sir Francis Drake High School, between Friends of Corte Madera Creek Watershed and the SEA DISC program of the school.  In addition, Kennard provided general watershed condition pictures.  All photos by Charles Kennard are copyrighted and for use in KRIS East Marin-Sonoma only.  Pictures in the Corte Madera Creek watershed by A.A. Rich and Associates were taken as a part of habitat typing and electrofishing surveys in 1999 (see Fisheries and Habitat Data by A.A. Rich and Associates).  In addition, the U.S. Army Corps of Engineers has compiled historical photographs of flooding conditions in Corte Madera Creek and some of these images were downloaded for inclusion in KRIS from     

The Novato and Miller Creek sub-basin in KRIS contain photos from Sue Lattanzio (Friends of Novato Creek), the Marin County Stormwater Pollution Prevention Program (MCSTOPPP), Prunuske Chatham Inc. and The Bay Institute (TBI).  Pictures provided by Sue Lattanzio show general watershed conditions in the upper and lower portions of the Novato Creek watershed.  MCSTOPPP provided historical pictures of Miller Creek, which show general conditions and restoration projects.  These include photos which were published in an environmental assessment by Environmental Science Associates in 1973.  MCSTOPPP also provided photos showing comparisons of stream conditions in Novato Creek from 1997 and 1987, with one picture from 1971.  Prunuske Chatham Inc. included photos of native riparian plantings and constructed wetlands and cross-levee pond in the Novato Creek watershed completed as mitigation for the Novato Creek Flood Control Project constructed by the Marin County Flood Control and Water Conservation District (PCI, 1999).  TBI's photos depict restoration projects coordinated by STRAW and MCSTOPPP (see description of Arroyo Corte Madera del Presidio photos above).  There are also maps provided in KRIS for the Novato Creek watershed, which show the results of an erosion inventory conducted by Prunuske Chatham Inc. in 2001 for the Marin County Department of Public Works (PCI, 2001).

Petaluma River watershed photos were provided by the National Ocean and Atmospheric Administration (NOAA) Restoration Center Image Catalog and Laurel Collins.  The NOAA pictures show a fish passage restoration project on Adobe Creek performed with the United Anglers of Casa Grande High School.  The images were downloaded from  In addition, KRIS contains aerials of San Antonio Creek depicting reaches where geomorphic assessments were performed by Laurel Collins for the Southern Sonoma Resource Conservation District in 2000 (see Geomorphic Studies by Laurel Collins).

The Sonoma Ecology Center and Laurel Collins provided photos for the Sonoma Creek watershed.  Pictures from the Sonoma Ecology Center highlight some of their watershed efforts, including continuous water quality and low flow monitoring, riparian and stream channel assessments, non-native vegetation removal, and stream clean-ups.  Laurel Collins provided images from her geomorphic assessments of Carriger Creek conducted in 2000 (see Geomorphic Studies by Laurel Collins).


EPA Landcover

The 1992 Land Cover data from the U.S. Environmental Protection agency was derived in cooperation with the U.S. Geologic Survey to produce a consistent, land cover data layer for the conterminous United States. The pixel resolution of the Landsat thematic mapper (TM) data is 30 meters. The coverage is useful in determining land use and landscape condition. One focus of this project is urbanizing or industrial areas because those types of land use have the greatest impacts on nearby streams. Classifications from EPA have been condensed to 14 categories from 20 by the IFR KRIS project to make for easier use in analysis. Both classifications are available in the KRIS East Marin-Sonoma Map project so they can be compared. Crop types in the irrigated areas were difficult to reliably distinguish; consequently, row crops are likely to be under represented. Since the image is now ten years old, the landscape may have changed considerable in the intervening years in some locations. For complete information, see the raw metadata dispensed with this project.


Vegetation and Timber Types of Cal Water Watersheds

The vegetation and timber types used in the KRIS East Marin-Sonoma project were derived from Landsat multi-spectral images taken in 1994. The U.S. Forest Service Pacific Southwest Region Remote Sensing Lab, in cooperation with the California Department of Forestry, analyzed the Landsat images to formulate a California wide electronic map layer of vegetation as part of the Northwest Forest Plan (Warbington et al., 1998). See background page for more information.

Stand conditions are represented with approximately 75% accuracy on a one hectare scale by the USFS vegetation data. Data is quarried for tree size or community type in ArcView (KRIS East Marin-Sonoma Maps). This allows quantitative assessment of vegetation types for seral stage based on tree size for geographic areas such as CalWater planning watersheds in the KRIS database. Not all watersheds within the KRIS East Marin-Sonoma project area are forested; consequently, only those CalWaters with some portion of the landscape in forest are characterized using these data. The EPA Land Cover data, also derived from the 1994 Landsat, is used to analyze watersheds comprised largely of grassland, pasture, agriculture or urbanizing areas (see below).

For use in KRIS, vegetation and timber types were simplified into ten classifications. Vegetation classifications are:

Very Large Trees = 40" in diameter or greater
Large Trees = 30-39.9" in diameter
Medium/Large Trees = 20-29.9" in diameter
Small/Medium Trees = 12-19.9" in diameter
Small Trees = 5-11.9" in diameter
Saplings = 1-4.9" in diameter
Non Forest = Non tree species such as shrubs, grasses or bare soil

The KRIS vegetation classification system is used in all KRIS East Marin-Sonoma planning watersheds to characterize riparian conditions. Ninety meter (297 ft.) zones of riparian influence are assigned to the 1:24000 stream layer in ArcView and only the vegetation within this zone is displayed and analyzed. This analysis tool indicates whether streams have trees bordering them or grass extending right up to the streams edge. Areas where livestock have open access to stream channels may be devoid of trees which would otherwise stabilize banks and provide a cooling influence through shade and microclimatic influences.

For more information on this overall subject, see the Background page on Vegetation.



Maps available in the KRIS East Marin-Sonoma project draw from many different sources of spatial data (see Cooperators). If you highlight a theme in the built-in KRIS Map viewer, a right click on the theme will allow access to full metadata. Data represent pertinent information for understanding conditions regarding anadromous fish and their habitat, including water quality. Map images are static on the Internet, although there may be clickable hot links to data or photos. When installed from CD on your computer, KRIS contains many features for working with spatial data (see Helps). The equivalent of complete Views (projects in ArcView) are represented in the database (from CD) in "MapMaster" topics, which are not available on the Internet. For people with ArcView, separate KRIS Maps CD can be acquired. 


Note about documents in KRIS