Key Basin Issues

Low flow and warm water temperatures during late summer and early fall are critical concerns throughout the SF Eel River Basin.  Low flows and high temperatures are due in part to increases in illegal water diversions (many for marijuana cultivation) and longer dry periods in the winter and early spring;

Streams throughout the Basin experience excessive sediment input from both anthropogenic and natural sources;

The morphology of the SF Eel River Basin has been changed due to erosion and aggradation;

Historic and current land use has altered natural watershed processes and conditions;

Alterations to watershed processes have affected the Basin both socially and economically;

Fish and wildlife have been adversely impacted by current watershed conditions in the Basin.

Responses to Assessment Questions

What are the history and trends of the size, distribution, and relative health and diversity of fish populations in the SF Eel River Basin?

The SF Eel River Basin supports populations of Chinook salmon, coho salmon, and steelhead trout;

There are two long term data sets for salmonid populations in the SF Eel River Basin: Benbow dam counts occurring from 1938-1975, and Van Arsdale counts beginning in 1933 and continuing today.  Trend lines for Chinook salmon, coho salmon, and steelhead trout abundance show significant decreases throughout the sampling duration;

Populations of all three salmonids appeared to decline abruptly following the 1955 and 1964 floods;

Current salmonid populations are not only less abundant, but they are less widely distributed than they were historically. Coho salmon have been documented in 59 tributaries (137 miles), Chinook salmon in 85 tributaries (195 miles), and steelhead trout in 120 tributaries (308 miles) throughout the Basin;

The Western Subbasin has the most widespread distribution of all three salmonid species, followed by the Eastern and Northern Subbasins;

The SF Eel River is one of six watersheds in CA that is recognized as a salmon stronghold under the North American Salmon Stronghold Partnership (NASSP).  Steelhead trout and coho salmon populations within the Basin have been identified as “strong populations”.  The health of stronghold watersheds must be maintained and enhanced if recovery is to succeed in the state of California;

The NMFS listed northern California runs of SONCC coho salmon (1997), CC Chinook (1999), and NC steelhead (2000) as threatened under the federal Endangered Species Act.  The California Fish and Game Commission also listed coho salmon as threatened in 2005;

The SF Eel River population of SONCC coho salmon is considered by NMFS to be a “functionally independent core population”.  These core populations are critical to recovery of salmon and steelhead throughout the ESU;

Sacramento pikeminnow, which were introduced into Lake Pillsbury in 1979, have been observed in many SF Eel River Basin surveys.  Pikeminnow feed on juvenile salmonids, particularly outmigrating salmonids (Moyle 2002), and compete with juvenile salmonids for food.  Pikeminnow prefer warmer water temperatures than native salmonids, therefore changes in the habitat that promote warmer water temperatures (such as loss of riparian vegetation, reduced pool depths, and reduced river flows) could promote Sacramento pikeminnow over salmonid species;

Adult SF Eel River salmonids use the lower mainstem Eel River as migratory route, and juveniles use the lower mainstem and estuary as rearing habitat.  South Fork Eel River Basin salmonids depend on these areas outside the Basin boundaries, and further information on watershed conditions in downriver habitat can be found in the Lower Eel River Basin Assessment Report.

What are the current salmonid habitat conditions in the SF Eel River Basin? How do these conditions compare to desired conditions?

Flow and Water Quality

Streamflow has been altered by both legal and illegal water diversion in riparian and upslope areas. Marijuana production is currently unregulated throughout the Basin, and is thought to be responsible for an increasing amount of diversion, particularly during low flow times;

Low summer flows and poor water quality are stressful to salmonids in tributaries;

Recent flow trends indicate that late summer flows are significantly lower than the historical running average, due to increases in both the number of diversions and quantity of water diverted from streams;

Excessive inputs of nutrients and pollutants, primarily from marijuana cultivation sites, are harmful to salmonids at all life stages in SF Eel River streams;

In 1999, the USEPA listed the SF Eel River as impaired due to elevated sedimentation/siltation and temperature;

Turbidity levels are high during winter rains, due to both anthropogenic and natural sediment inputs.  These winter rainfall events correspond to spawning season for SF Eel River salmonids.


Soils in surveyed reaches of streams in the South Fork Eel Basin are prone to erosion, and slides have been observed to contribute fine sediment to the streams;

Sediment from improperly constructed roads and construction around marijuana grow sites enters watercourses throughout the rainy season;

Several tributaries are usually isolated from the mainstem S.F. Eel River by subsurface flows in late summer and early fall due in part to aggregation of bedload materials at the confluence;

Riparian Condition/Water Temperature

The Humboldt County Resource Conservation District collected water temperatures in the SF Eel River mainstem and selected tributary locations between 1996 and 2003, and reported mostly good temperatures in Western Subbasin streams and  unsuitable/poor conditions for salmonids in most Northern and Eastern Subbasin, and mainstem locations (maximum temps ranged from 73ºF–76ºF);

The USGS monitors instream temperature at two locations in the SF Eel River Basin: Cahto Creek and Elder Creek, both in the southern part of the Basin.  Data is available beginning in October 2007, and temperatures at both locations were unsuitable for salmonids during late summer months, but did not reach lethal levels (≥75˚F) at any time;

Upper tributaries near Branscomb provided cold water refugia areas for SF Eel River salmonids;

Temperatures recorded in the lower mainstem SF Eel River near Phillipsville and Miranda were highly stressful for salmonids;

Salmonids may seek refuge in thermally stratified pools or in localized refugia provided by surface and groundwater interactions when mainstem and tributary temperatures reach stressful or even lethal temperatures;

Nearly 75% of the total length of tributary reaches surveyed by CDFW crews between 2000 and 2010 met the target value of 80% canopy coverage. Riparian canopy density suitability increased in all subbasins between 1990-1999 and 2000-2010;

Deciduous trees made up a greater percentage of canopy vegetation than coniferous trees in all subbasins, and the relative proportion of coniferous vegetation to deciduous vegetation increased in all subbasins over time.

Instream Habitat

Overall habitat suitability (based on canopy density, pool depth, pool shelter complexity, and substrate embeddedness values) was low in all subbasins during the two time periods (1990-1999 and 2000-2010), but scores improved in Western and Northern Subbasins (and in the SF Eel River Basin as a whole) over time;

Pool depths were considered poor for salmonids in all CDFW surveyed streams in the Basin, although suitability increased slightly over time in Western Subbasin streams;

Quality pool structure is lacking in streams throughout the Basin; no surveyed streams met standards for pool shelter, and pool shelter values decreased in nearly all streams over time;

Average percent shelter from LWD was low (<5%) in all three subbasins, indicating a lack of holding and rearing habitat for adult and juvenile salmonids during low and high flow times;

Large woody debris is generally lacking in many areas of the Basin, particularly in Eastern Subbasin streams.


Both fine and coarse sediment input are concerns in the Basin, with sediment input from both natural and anthropogenic sources, and from large historical flood events;

SF Eel River stream beds have been described as heavily silted due to increased sedimentation, and natural stream morpology has been altered by aggradation throughout the Basin;

Cobble embeddedness suitability increased in all subbasins, and in the SF Eel River Basin as a whole, when comparing habitat data collected between 1990-1999 and 2000-2010.  Although category 1 embeddedness values were suitable, they were still below target values (50%) for all subbasins using data collected during both time periods;

Areas of suitable spawning gravel are very limited throughout the Basin.

Refugia Areas

There are few high quality refugia streams in the SF Eel River Basin: one in the Northern Subbasin (Squaw Creek), one in the Eastern Subbasin (Elder Creek), and three in the Western Subbasin (Indian, Low Gap, and Upper Hollow Tree Creeks);

Western Subbasin streams provide the most high potential refugia areas, especially in the Hollow Tree Creek Basin;

Eastern Subbasin streams provide mostly medium potential and low quality stream refugia, with more low quality areas in the northern part of the subbasin, and medium potential areas in most southern streams in the Tenmile Creek and Rattlesnake Creek Basins;

The Northern Subbasin contains a variety of refugia streams, ranging from high potential in Bull Creek, to low quality in Salmon, Fish, and Ohman Creeks.


What watershed and habitat improvement activities would most likely lead toward more desirable conditions in a timely, cost effective manner?

Flow and Water Quality Improvement Activities

Protect stream flows from diversion, particularly in low flow summer months. Programs that will encourage landowners to store water during high flow times and stop diverting from streams during low flow times are being developed by SRF and HSU in Redwood Creek, and could be expanded to other areas in the Basin;

Reduce fertilizer, pesticide, and fine sediment input from marijuana cultivation operations;

Reduce fine sediment input and restrict illegal grading operations from unpermitted residential development sites;

Where necessary, identify barriers to fish migration in the form of large debris accumulations, culverts, etc. and modify them.

Erosion and Sediment Delivery Reduction Activities

Continue to support and expand the scope of road decommissioning projects funded through FRGP and other sources, in order to reduce fine sediment input to streams from unused roads;

Conduct an upslope erosion inventory on subbasin streams in order to identify and map stream bank and road-related sediment sources. Sites should be prioritized and improved in order to decrease sediment contributions throughout the Basin;

Identify and rehabilitate illegal road grading, construction, or clearing activities associated with residential development and/or marijuana cultivation operations in order to reduce the amount of fine sediment entering streams;

Continue to work with timber companies to ensure that sediment reduction plans are in place for harvested areas, roads, and surrounding areas;

Reduce the potential for fine sediment input following catastrophic fires by using prescribed burns to reducing fuel loads.

Riparian and Habitat Improvement Activities

“Riparian right” water diversions should be monitored and storage requirements modified so diversion is not taking place during low flow times.

Voluntary conservation programs designed to reduce diversions, similar to those being developed by SRF and HSU in Redwood Creek, should be expanded and applied in additional streams with known fish presence throughout the SF Eel River Basin;

Enforce grading ordinances in Humboldt and Mendocino Counties to protect riparian vegetation, and to protect against sediment delivery from unpermitted development sites. Grading ordinances have been developed and are currently in effect but many developments throughout the SF Eel River Basin are unpermitted and therefore unregulated;

Riparian buffer should be allowed to grow/re-grow along streambanks – in areas with exposed stream banks, riparian planting projects could be completed to increase bank stability;

Programs to increase riparian vegetation should be implemented in areas where shade canopy is below the target value of 80% coverage, particularly in areas of Tenmile Creek in the Eastern Subbasin;

In creeks where fish spawning and rearing habitat is limited, pool enhancement and instream structures should be added to increase complexity;

In streams where pool habitat is limited, enhancement structures such as LWD or boulders that encourage scour should be added to increase the amount of pool habitat and depth in existing pools;

In streams where spawning area is limited, projects should be designed to trap and sort spawning gravels in order to expand and enhance redd distribution;

Log debris accumulations in streams that retain high levels of fine sediment should be assessed, and carefully removed where appropriate.

Education, Research, and Monitoring Activities

Develop long-term flow monitoring studies to better understand water usage and diversion patterns for residences and industrial marijuana growing operations, particularly during low flow times;

Partner with private agencies, community groups, local residents, and academic institutions to educate residents about water usage patterns and trends, and to develop conservation and/or storage plans to reduce diversion and improve water quality and quantity;

Because water quality data are limited, monitoring of summer water temperatures should be performed over at least a three to five year period;

Support the HCRCD and Eel River Recovery Project in their ongoing efforts to monitor and improve habitat and water quality in the Basin;

Water quality data, including temperature and dissolved oxygen, should be consistently collected by land owners and responsible agencies throughout the year, for several years, in order to accurately characterize instream conditions;

Implement biological monitoring of aquatic invertebrates and food web dynamics to better understand instream food sources and availability for salmonids at all life stages;

CDFW stream habitat surveys provide information only for reaches accessible to anadromous salmonids. Additional surveys above the limits to anadromy are necessary to identify upstream conditions that affect fish bearing downstream reaches, including riparian canopy condition or sediment delivery sites that may benefit from erosion control treatments;

Where necessary, identify barriers to fish migration in the form of large debris accumulations, culverts, etc. and modify them to allow fish passage;

Continue to conduct habitat and fish inventories on streams in the Northern, Eastern, and Western Subbasins, to assess changes in habitat suitability over time;

Reduce the risk of human-caused fire by limiting access to high fire danger areas, in conjunction with annual prescribed fire treatment in high use areas and public education efforts;

Continue to support local educational programs such as the June, 2013 construction of a “willow wall” to increase bank stabilization and improve salmonid habitat in Bull Creek. This project was completed by the CCC Watershed Stewards program staff and the Eel River Watershed Improvement Group as part of the Creek Days Environmental Education Fair.

Partner with local academic institutions and private agencies as a means to encourage the study of the fish and corresponding habitat.