Salmon Creek Estuary Restoration and Monitoring Results

Summer 2015 Ecesis, Volume 25, Issue 2

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A collaborative effort to restore the Salmon Creek Estuary at Humboldt Bay National Wildlife Refuge, south of Eureka, California, has come a long way and led to interesting results. This article describes the process of recreating a diversity of estuarine habitats within an altered landscape, some results of biological and water quality monitoring, and drought-related observations.

Over a century ago, the complex network of tidal channels and marshes of Humboldt Bay was diked and drained for cattle grazing. Meandering streams were consolidated, straightened, and greatly reduced while marshlands were drained. Salmon Creek, the largest tributary to Humboldt Bay, was ditched and the channel isolated from tidal influence of the bay using tide gates. In following years the drained marsh plains subsided and the coho salmon runs plummeted. Today, about 90% of Humboldt Bay’s historic salt marsh and estuarine habitat has been lost.

Research and monitoring in Humboldt Bay and elsewhere has increasingly demonstrated the importance of tidal estuaries and connected low gradient freshwater wetlands, side channels, and other slow-water areas in the life history of coho salmon and other sensitive fish species such as tidewater goby, steelhead and coastal cutthroat trout. 

Salmon Creek Estuary was incorporated into Humboldt Bay National Wildlife Refuge in the 1980s. In 2001, restoration planning began for Salmon Creek Estuary on the Refuge. The goals were to improve the structure, function, and diversity of the degraded estuary while working within the physical constraints and multi-species management objectives of the Refuge. These goals were pursued through a collaborative effort in multiple phases. 

Phase I

As part of the first phase of restoration, the antiquated tide gate system in lower Salmon Creek was modernized in an effort to improve estuary habitat and fish passage. For example, an additional connection between Humboldt Bay’s Hookton Slough and Salmon Creek was restored with the construction of a major new tide gate in an existing levee. Also, several small outmoded tide gates were replaced. The new adjustable tide gates are designed with larger openings to increase flow capacity, decrease water speed, and allow for unimpeded fish passage. They also are designed to greatly increase tidal circulation into and out of the estuary, which is a key to improving habitat by improving water quality (increasing oxygen content) and flushing sediment. Increased sediment transport to the ocean is expected to restore channel capacity — by widening and deepening channels — and decrease flooding upstream. Water circulation improvement is designed to allow additional seasonal rearing of salmonids in the lower 8,500 foot reach of Salmon Creek. Also, the muted tide cycle helps enlarge the size of this vital South Humboldt Bay estuary. The upper boundary of tidal influence moved upstream into the Refuge and increased the acreage of tidal wetlands by another 13 acres. Construction and installation of the new tide gates was performed by Nehalem Marine. Pacific Coast Fish, Wildlife and Wetlands Restoration Association (PCFWWRA) provided much of the project management and grant administration. Funding for this phase was provided by California Department of Fish and Wildlife’s (CDFW) Fisheries Restoration Grant Program and California Coastal Salmon Recovery Program, US Fish and Wildlife Service (USFWS) Coastal Program, Humboldt Bay National Wildlife Refuge and California Coastal Conservancy. 

Phases II & III

The second and third phases, from 2010-2013, restored 29.79 acres of estuarine habitat, including:

  • Approximately 10,500 feet of meandering estuarine channel and six tidally influenced off-channel and side-channel ponds were constructed in order to restore habitat in an area that was historically ditched and drained for agriculture. Most of these are in the upper reach of tidal influence and include a stable channel form, complexity, sinuosity, and efficient routing of sediment and flood waters. An extra upstream pond was added to Phase III because biological monitoring showed that coho salmon preferred the ponds furthest upstream with the lowest salinities.
  • Nearly 15.5 acres of subsided lands were raised to tidal salt marsh elevation with spoils generated from channel and pond excavation.
  • Sixty-one large wood structures were installed in the channel and ponds to provide channel structure and fish habitat diversity.
  • A fish passage structure was constructed in the Refuge’s passive water delivery system to reduce existing stranding potential and allow access to suitable habitat in the northern part of the Refuge during higher water events.
  • Riparian vegetation was planted near the newly constructed channels and ponds as appropriate.

Funding and staff expertise was provided by the USFWS Coastal Program. Substantial grant funding was also provided by CDFW’s Fisheries Restoration Grant Program, National Fish and Wildlife Foundation, and Ducks Unlimited through a North American Wetland Conservation Act grant. Contributions of equipment and operators from the USFWS Maintenance Action Program reduced the amount of grant funding needed. Project Partners also included: PCFWWRA, Michael Love and Associates, Trinity Associates Environmental Planning, Pacific Watershed Associates, Humboldt Fish Action Council, California Conservation Corps, Restoration Forestry, Wallace Structures, SHN Consulting Engineers & Geologists Inc., Wayne Bare Trucking, Frank Zabel Trucking, Wendt Construction, California Redwood Company, and planting volunteers. 


In 2005, CDFW began sampling the stream-estuary ecotone of Salmon Creek to document its use by juvenile salmonids and to assess estuarine habitat restoration. The monitoring has consisted of bi-weekly fish and water quality sampling. CDFW captures fish using seine nets and minnow traps baited with frozen salmon roe. They also operate PIT tag antenna stations to remotely detect PIT-tagged salmonids moving in and out of ponds. Water quality monitoring has involved collecting water temperature, salinity, and dissolved oxygen data throughout the water column with a hand-held Yellow Springs Instruments Professional Plus meter at standard locations in the main Salmon Creek channel and off-channel ponds. 

CDFW’s monitoring has found that during the late summer and early fall the Salmon Creek stream-estuary ecotone has high water temperatures and salinity and relatively low dissolved oxygen making it unsuitable for juvenile salmonids. Then, in average or wetter rainfall years, increased stream flows flush saltwater from the stream-estuary ecotone during the winter and spring and create more preferred freshwater habitat for juvenile salmonids. When flows begin to drop in the spring and brackish water begins to move into the stream-estuary ecotone, there is usually a surface freshwater layer providing habitat for juvenile salmonids. Eventually stream flows drop to low levels by late spring resulting in brackish water conditions throughout the stream-estuary ecotone. Virtually all rearing juvenile salmonids leave the stream-estuary ecotone by June.

According to CDFW’s report in 2013, based on data from Salmon Creek and other Humboldt Bay tributaries through 2012, mean growth rates of juvenile salmonids in the ecotone were typically 0.15 to 0.25 mm/day which was higher than growth rates observed by other projects in stream habitat upstream of the ecotone. Juvenile salmonids sought out freshwater rather than brackish water habitat while rearing in the ecotone. Juvenile salmonids, especially coho salmon, utilized newly constructed off-channel ponds as soon as they were completed and fall and winter rains increased stream flows and converted the ponds to primarily freshwater habitat. CDFW concluded that the stream-estuary ecotone provides productive rearing habitat for juvenile salmonids, especially over-winter habitat for juvenile coho salmon.

During the recent drought, monitoring results changed, and the typical estuary ecotone dynamic described above altered. More juvenile coho were captured in 2011/2012 than in subsequent drought years. For much of 2014, the ongoing drought resulted in unsuitable water quality for juvenile salmonids in the Salmon Creek ponds. During 2014, water temperature and salinity were higher than previous years, especially during the spring to early summer rearing period. Also, dissolved oxygen was generally lower in 2014 than previous years. These conditions were likely caused by the drought resulting in lower stream flows entering the Salmon Creek stream-estuary ecotone that allowed saltwater to intrude into Salmon Creek at higher concentrations and for longer periods of time. For example, in 2012, the last average rainfall year, freshwater conditions persisted throughout the water column through May, and surface freshwater was still present in June, but in 2014 the water column was stratified by April and brackish water was present throughout the water column by May. By August 2014 CDFW detected hyper-saline conditions of 38 ppt throughout the water column of Salmon Creek. This was the highest salinity reading detected since CDFW began sampling in 2005. Even after rainfall started in November, a layer of brackish water with low dissolved oxygen remained along the bottom of the ponds until at least mid-December.

CDFW captured and detected substantially less juvenile coho salmon in the Salmon Creek stream-estuary ecotone in 2014 compared to 2012, when habitat conditions were most favorable to support them (15 captured or detected by PIT tag in 2014 versus 170 in 2012). From July to December 2014, no salmonids were captured. But on the bright side, the restoration project appears to be benefiting federally listed as endangered tidewater goby and a variety of other coastal creatures which thrive in brackish conditions. From July to December 2014, 1,618 tidewater goby as well as top smelt, surf smelt, shiner surfperch, threespine stickleback, bay pipefish, Pacific staghorn sculpin, prickly sculpin, unidentified juvenile sculpin, plainfin midshipman, starry flounder, juvenile Dungeness crab, and yellow shore crab were detected in the Salmon Creek Estuary project area.

Many other case studies discuss the effect of the drought on stream flows and water temperature but this study is one of the few to document the effect of the drought in stream-estuary ecotone habitat, primarily in the form of higher concentrations of water salinity and the increased duration of brackish water in the stream-estuary ecotone. The monitoring has emphasized the importance of restoring a variety of habitats and allowing species to move in space and time to find their niche, as conditions change. This project emphasizes that a multi-species approach in restoration is important, as well as long-term monitoring program. 

Figure 8. Fish species present in Salmon Creek estuary that are listed under State and Federally Endangered Species Acts (ESA): Southern Oregon Northern California Coast coho salmon which are listed under the State and Federal ESA as “Threatened”, and Northern California steelhead trout which are listed as “Threatened” under the Federal ESA; there is also a substantial population of tidewater goby that is listed as “Endangered” under the Federal ESA and a small number of longfin smelt which is listed as “Threatened” under the State ESA. — Laura Bridy, Pacific Coast Fish, Wildlife and Wetlands Restoration Association, with contributions from Michael Love and Associates and California Department of Fish and Wildlife

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