Bibliography Background About KRIS

KRIS Humboldt Bay InfoLinks

Humboldt Fish Action Council Adult Salmon Trap Data

The Humboldt Fish Action Council (HFAC) collected data related to operation of their Freshwater Creek weir that traps adult coho and chinook salmon. HFAC captured salmon for small scale hatchery operation beginning in 1978 and fertilized eggs from the hatchery operation at Mad River Hatchery, where juveniles were reared to the fry stage. HFAC then transported the juvenile salmon to rearing ponds in McCready Gulch in the Freshwater Creek drainage. The primary emphasis of the HFAC hatchery in the late 1980's and early 1990's was coho salmon enhancement. Juvenile coho from the hatchery operation were planted in Graham Gulch, McCready Gulch and other Freshwater Creek tributaries. These fish of hatchery origin may influence abundance of coho and the fish community structure of tributaries planted. Because coho salmon populations in Freshwater Creek in the early 1990's appeared near carrying capacity, the emphasis of the HFAC hatchery shifted to chinook salmon only.

The HFAC Freshwater trap counts include the number and species of fish intercepted. Adult salmon have been trapped from November through January, however, the number of days of trap operation varied. The flows in Freshwater Creek also effect trap efficiency as fish may avoid the trap during high flows. Because of these variables, the HFAC trap counts cannot be expanded to estimate populations in any year or for trends over time.

The Institute for River Ecosystems, which is affiliated with Humboldt State University, has provided support for HFAC since 2002 and now is the repository for data. They contributed many photographs of trap operations, now accessible in the KRIS photo database pages. HFAC accepts public donations through its Adopt-a-Fish program.

Downstream Migrant Trapping, Spawner Surveys and Adult Population Estimates

Freshwater Creek fisheries are more well studied than those of any other Humboldt Bay tributary or those of most other coastal streams in northwestern California. The richness of data is owing to the number of agencies and entities that have collaborated since 1986. The Humboldt Fish Action Council, a nonprofit group, not only operated an adult salmon trapping weir for capture of broodstock for artificial propagation, but also began operation of downstream migrant traps and conducting adult salmon and redd counts in 1986. Since then, HFAC has had assistance from and cooperation with the California Department of Fish and Game, the Americorp Stewards program, the Pacific Lumber Company and the Institute for River Ecosystems at Humboldt State University.

Downstream Migrant Trapping: HFAC and its many cooperators have used pipe traps sometimes in combination with fyke nets to capture downstream migrating salmonids. For details on trapping methods and locations of traps see Duncan-Vaughn (1996) and Ricker (2001, 2003a, 2003b, 2005a). Data are collected and shared in different ways in different years, so not all species of fish are counted in some years as recent surveys give results for salmonids only. Analysis of data, however, has increased with confidence intervals and standard error calculated on numbers of fish emigrating in some years. California Department of Fish and Game reports include trap efficiencies and length frequency for various salmonid species captured.

Adult Carcass, Live Fish and Redd Counts: Cooperative adult salmon, carcass and redd surveys vary in terms of effectiveness depending on flow year, frequency of storm events and turbidity. Effort on various reaches of Freshwater Creek have varied between years. The California Department of Fish and Game combined marking and tagging so that surveys could have a marked population for use in Peterson mark-recapture estimates.

Adult Population Estimates: Recent work by CDFG includes population estimates for chinook, coho and steelhead in 2002-2003 (Ricker, 2005e) and 2004-2005 (2005f) and for adult steelhead in 2000-2001 (Ricker, 2002) and 2001-2002 (Ricker, 2005g). Adult steelhead were tagged at the Freshwater Creek weir and then recapture at downstream migrant traps and or counted in carcass surveys. See California Department of Fish and game reports for more information on methods and results.

See Fish Population Background page for more further information on how fish populations are assessed or for regional fish Pacific salmon status.

Elk River Adult Coho and Chinook Salmon Spawner Counts

The California Department of Fish and Game conducted spawner surveys in the Elk River basin 1985 to 1994. The most intensive effort occurred in the spawning seasons from 1986/87 to 1988/89. Carcass and redd counts or those of live adult spawners can be compromised by high flows that prevent access for surveys and by high turbidity, which obscures redds and fish. No recent data are available for Elk River salmon and steelhead are available and the data presented here may not be representative of present existing runs to changes in aquatic habitat related to sedimentation.

Elk River Electrofishing and Downstream Migrant Trapping Data

Juvenile salmon and steelhead data for Elk River come from two sources: electrofishing samples collected as part of habitat typing surveys and downstream migrant trapping data. Electrofishing done without block nets or multiple passes cannot be used to assess standing crops or populations, but structure of samples can be used to understand aquatic health and biodiversity. Because samples are collected during low flow periods in summer and fall, they would miss juvenile chinook because of their early emigration. Therefore, absence of juvenile chinook in samples does not indicate lack of use by adults for spawning. A downstream migrant trap was operated by Larry Preston of CDFG in 1988 on the North Fork Elk River:

" The trap was installed one mile above the North and South fork confluence. This site is well below most spawning areas. A total of 31 trap days was made from March 29 through July 1, 1988 (95 days). A total of 10,920 YOY, 695 1+, and one 2+ coho were captured. Three coastal cutthroat (98, 99, 180 mm), sixty-three steelhead (four YOY, 30-32 mm; 53 yearlings, 72-175 mm; one age two-plus 230 mm; and 3 adults, 42, 45, and 85 cm and l unmeasured), 18 sculpin, 113 lamprey (107 ammocoetes and 6 adults), and 159 sticklebacks were also sampled. The number of coho 0+ leaving the North Fork was thought to be an anomaly but our trapping results were similar to Freshwater Creek and Mendocino streams. One explanation for the 0+ coho emigration was limited habitat availability. Flows were abnormally low during spring 1988, resulting from the second consecutive drought year. The zero-plus coho ranged from 24-48 mm. The age one-plus coho ranged from 53-128 mm. The peak emigration was May 31,1988 which followed a major storm event. However, the study showed a consistent departure of 1+ coho throughout the sample period. Only one 2+ (165 mm) coho was observed."

Downstream migrant traps collect data on salmonids and other fishes as they migrate downstream over a period of months or weeks. These samples would include chinook salmon juveniles, however, larger fish such as older age steelhead juveniles or cutthroat trout may be able to avoid downstream migrant traps. Trap avoidance can result in underestimation of some species or age classes in this type of sample.

Aquatic Macroinvertebrate Indices for Humboldt Bay Tributaries

Aquatic insect data presented in KRIS Humboldt Bay comes from the Pacific Lumber Company Habitat Conservation Plan (1998) and from work associated with the Freshwater Creek Watershed Analysis (PL, 2002). The HCP data are for all Humboldt Bay tributaries and all of the PL ownership and include samples collected from 1994-1996. Results for all stations were not provided for all years. Data for Freshwater Creek for all stations from 1997-1999 were provided as part of cooperative Freshwater WA participatory studies. Samples were collected using a kick net and preserved in alcohol then identified to species or the lowest possible taxonomic order by an aquatic entomologist, John Lee. Sample collection and identification followed the California Stream RAPID Bioassessment Procedure (Harrington, 1996). If more than one sample was available for a given site, the values were averaged. Methods were very similar to the Humboldt County RCD's Eel River Water Quality Monitoring Study, where aquatic insects were collected from 22 Eel River tributaries (Friedrichsen, 1998).

The aquatic insect indexes used in studies displayed in KRIS Humboldt Bay are Richness, EPT, and Percent Dominant Taxa. The Richness Index is simply the total number of taxa or species present. The diversity of aquatic insects decreases as water quality problems increase. The EPT Index is the number of species at a given location of the pollution intolerant orders Ephemeroptera, Plectoptera, and Trichoptera, more commonly known as mayflies, stoneflies and caddisflies. The Percent Dominant Taxa is calculated by dividing the number insects of the most abundant species by the total number of organisms in the entire sample. Collections dominated by one taxa represent a very disturbed ecosystem, while those with many taxa of nearly equal abundance indicate an undisturbed one.

Reference lines on aquatic macroinvertebrate charts in KRIS Humboldt Bay are based on the California Department of Fish and Game Benthic Macroinvertebrate Index (BMI) developed for the Russian River (Harrington, 1999). Harrington (1999) uses five metrics including the Simpson and Hillsenhoff Diversity indices in addition to the three used in KRIS Humboldt Bay but scores the range of community diversity and aquatic health for use within the IBI as follows:

High Diversity/Good Health
Intermediate Diversity/Health
Low Diversity/Poor Health
Taxa Richness
>= 36
EPT Taxa
>= 25
<= 12
Percent Dominant Taxa
<= 14%
>= 39%

See the Aquatic Insect Background page for more information.

Road Densities in Humboldt Bay Watersheds

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 filling pools and diminishing habitat diversity. See the Road Background page for discussion of references show on charts and for more information on the relationship of road density and aquatic health. Road data in KRIS Humboldt Bay were acquired from Legacy the Landscape Connection, which created a seamless north coast coverage for roads at a 1:24000 scale. Original data sources include the California Department of Forestry, the U.S. Forest Service, the U.S. Geologic Survey and other sources in the public domain.

After integrating the data from Legacy, Dr. Paul Trichilo of the Institute for Fisheries Resources calculated summary statistics for analysis, including road density in miles per square mile, total road-stream crossings and road crossings per stream mile. Road data on timberlands include main haul; roads only; therefore, skid trails, temporary roads and and landings are not represented. Likewise, USGS 1:24000 stream data are also under-represent actual Humboldt Bay tributaries. The incomplete nature of the road and stream layers lead to a conservative estimate of culverts and crossings. Streams may flow beneath city streets in culverts; consequently, there may be few stream crossings in urbanized Calwater Planning Watersheds surrounding Humboldt Bay.

Fine Sediment in Humboldt Bay Tributaries

Data in KRIS Humboldt Bay on fine sediment is from sediment samples taken by the Pacific Lumber (PL) Company as part of their Habitat Conservation Plan (PL, 1998) and in Freshwater Creek from a Master's Thesis by Barnard (1992) and from the Freshwater Creek Watershed Analysis (PL, 2002). Data prior to 1997 were not made available in electronic form and were entered by hand for the previous KRIS Coho project. Data for Freshwater Creek were made available for the years 1997-1999 as part analytical activities related to the Freshwater Creek WA (PL, 2002).

PL collected fine sediment data using bulk gravel samples which can be collected using either a shovel or core sampler known as a McNeil sampler. Gravel samples are then run through sieves and ultimately the smallest fraction into a filter. The PL HCP (1998) and Freshwater WA (2002) do not specify whether shovel samples or McNeil samples were used in different years, but studies indicate that these sampling techniques give very similar results (Schuett Hames et al., 1996). The thresholds shown for levels of fine sediment of 14% for sizes less than 0.85 mm and 30% for fines less than 6.4 mm come from the U.S. Environmental Protection Agency (1998). These standards have been applied to most other sediment impaired coastal basins. The use of these standards in KRIS Humboldt Bay is only for comparison. PALCO has chosen to sample for fines less than 4.7 mm which underestimates the problems with small gravel sized particles that can infiltrate between cobbles and cap redds. See Sediment Background page for more information.

Turbidity Threshold Sampling in Humboldt Bay Tributaries

Turbidity is a change in the optical property of water which causes light to be scattered and absorbed as opposed to transmitted in straight lines (APHA, 1980). Turbidity may be caused by suspended sediments such as silts or clays, fine particulate organic material or microorganisms such as plankton. Turbidity threshold sampling uses automated equipment to measure turbidity and collect suspended sediment samples. Data are collected using a programmable data logger, a turbidimeter mounted in the stream, a pumping sampler, and a stage-measuring device as described on the Redwood Science Lab website (

There has been significant amount of turbidity threshold sampling conducted in Humboldt Bay. Data collectors include the non-profit group Salmon Forever, the U.S. Forest Service Redwood Sciences Laboratory, PALCO, and Randy Klein Consulting. In addition to data, Salmon Forever provided a Quality Assurance Project Plan (Salmon Forever, 2001) and summary of its 2005 sampling. When PALCO provided its 2003 data to the North Coast Regional Water Quality Control Board, it included summaries for Elk River and Freshwater that list locations of sampling stations and provide a key to data quality codes. PALCO also provided a summary of data quality for its Elk River 2003 data. Manka (2005) describes results of monitoring in three tributaries of Elk River. Salmon Forever and Redwood Science Lab also provided photos of their sampling sites, accessible through the KRIS photo database pages.

KRIS includes an online zoomable map of TTS monitoring locations in Humboldt Bay watersheds.

An important aspect of turbidity is that it can impair fish feeding and Sigler et al. (1984) found that steelhead growth was limited when turbidity rose over 25 nephlometric turbidity units (ntu). Newcombe and MacDonald (1991) point out that the duration of high turbidity is an important factor in stress to aquatic organisms. The U.S. Geological Survey (Miller, 2004) has recommended that NTUs by split into a variety of different units based on difference in the design of sampling equipment (see Sediment Background page for more information). Klein (2003) recently published results of a study including tributaries of Humboldt Bay showing relationships between management and levels and duration of turbidity.

Climate and Rainfall Data

Climate data available in the KRIS Humboldt Bay project come from the California Data Exchange Center (CDEC) database. The 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 Precipitation Background page.

Measuring Sediment in Pools (V*) in Freshwater Creek and 60 Other Northern California Coastal Streams

The proportion of a pool's residual volume that is filled by fine sediment is termed V-star (Hilton and Lisle, 1993). Excessive fine sediment fills pools and causes general instability of stream gravels and channel form (Montgomery and Dietrich, 1994). The Pacific Lumber Company (2002) Freshwater Creek Watershed Analysis lead to collection of V* by Pacific Watershed Associates in 1999 at the same location as measured by Knopp (1993) in 1992 and 1993. This location is on the mainstem Freshwater Creek above the South Fork. Regional TMDL's (U.S. EPA, 1998) set the target for fine sediment in pools as a V* value of 0.21 that is shown as a reference on all charts of V* in KRIS Humboldt Bay.

Loss of pool depth and volume as well as channel complexity lowers the carrying capacity of streams for aquatic biota, including salmonids (Reeves et al, 1993). Various indices for measuring such impairment of stream channels were tested by Knopp (1993) at 60 northwestern California sites. V* values from all northwestern California results are displayed in KRIS Humboldt Bay. See the Sediment Background page to learn more.

Water Temperature in Freshwater Creek 1998-1999

Because the Humboldt Bay watershed is very influenced by marine air masses and summer fog, water temperature is generally not limiting for salmonids; consequently, there are not much water temperature data in KRIS Humboldt Bay. Temperature data for the project are only available for Freshwater Creek where data were released for the Pacific Lumber Company (2002) Freshwater Creek Watershed Analysis. For more information on Pacific salmon and water temperature, see the Temperature Background page.

Humboldt Watershed Council Photographs

The Humboldt Watershed Council and its members from Elk River and Freshwater Creek contributed photos for KRIS Coho taken mostly from 1996-1998, although there also shared pictures of salmon fishing in lower Freshwater Creek in the 1970's. The KRIS Coho project collected information from watersheds affected by the Pacific Lumber Company Habitat Conservation Plan. Doug Thron contributed photos for use in KRIS projects in support of the HWC and its members. His photos are copyrighted and anyone intending to use them outside KRIS projects should contact Doug Thron Nature Photography.

Habitat Typing Surveys

California Department of Fish and Game (CDFG) conducted habitat typing surveys in the Elk River and Freshwater Creek watersheds between 1994 and 1996. CDFG surveys provide an inventory of stream conditions in both quantitative and qualitative form. Protocols follow the California Salmonid Restoration Manual (CDFG, 1998). Summary data by reach is used in KRIS which was derived from paper reports supplied by CDFG. To learn more about using fish habitat data, check the Habitat Typing Background page.

Photographs from the Institute for Fisheries Resources KRIS Project Office

Pat Higgins and Eli Asarain of the Institute for Fisheries Resources KRIS project office in Arcata, California contributed photos to the KRIS Humboldt Bay database. These photos are digital and captured at an approximate 1 megabyte in size, but reduced for incorporation into KRIS. Most photos were taken during high flow or flood events and show Freshwater Creek, Janes Creek, Ryan Slough, Elk River, Salmon Creek and Jacoby Creek.

Photographs from Northwest Emergency Assistance Program (NEAP) Restoration Projects

These photos were scanned from a report on restoration projects in Graham Gulch, tributary of Freshwater Creek, funded through the Northwest Emergency Assistance Program (NEAP). The report and others on similar projects are available from the Humboldt County RCD.

Vegetation and Tree Size Classes and Change Detection Using Landsat Imagery

Data regarding vegetation, tree size, timber types are derived from a Landsat multi-spectral image taken in 1994 analyzed by Humboldt State University and more recent data for 1999 from the U.S. Forest Service (USFS) Sacramento Remote Sensing Lab in cooperation with the California Department of Forestry's (CDF) Fire and Resource Assessment Program (FRAP). The USFS and CDF also work cooperatively to assess California Statewide changes in vegetation in association with the Northwest Forest Plan (Warbington et al., 1998; Levien et al., 2002) and change scene detection for the Humboldt Bay watershed is available using 1994 and 1998 Landsat. The Landsat derived vegetation data for northwestern California and the Humboldt Bay watershed are accurate to a one hectare scale. While these data scale is coarse, data have been checked using a number of different methods. Because the scale of the vegetation GIS is one hectare, individual large trees may not show up when using this analysis tool. See Vegetation Types Background page for more information on Landsat data interpretation.

The KRIS project chose a 100 meter (328 foot) distance as a zone of biological influence for the riparian corridor based on Spence et al. (1996). This represents approximately two site potential tree heights as recognized by FEMAT (1993). Data may not pick up individual large trees or narrow buffer strips retained during timber harvest, if they do not comprise a significant portion of a hectare. The age and size of the trees at the water's edge and buffer area are, however, represented accurately enough to be used as reconnaissance tools for estimating potential effects on microclimate, stream temperature influence and large wood recruitment potential.

KRIS Humboldt Bay Maps

Spatial data from many sources was assimilated for the KRIS Humboldt Bay project to provide a desk top tool for watershed analysis, when installed on a computer hard drive, or as maps on the Internet ( Data from various sources were acquired by Dr. Paul Trichilo of the Institute for Fisheries Resources KRIS project along with metadata and associated reports. IFR created theme legends for ArcView and KRIS Humboldt Bay database applications. Right click each theme in the KRIS Map Viewer to see full metadata for each data type. Data sources include Humboldt State University, U.S. Forest Service, California Department of Forestry, U.S. Geologic Survey, Legacy the landscape Connection, Redwood Community Action Agency and the City of Arcata.

Note about documents in KRIS