Observations of Salmonid Use, Water Quality, and Channel Morphology of the Navarro River Estuary/Lagoon
May, 1996 to December, 1997

Draft Project Summary
Stephen P. Cannata

This study was conducted to collect data describing estuarine utilization by steelhead trout (Oncorhynchus mykiss) and coho salmon (O. kisutch) and to characterize habitat conditions in the Navarro River estuary/lagoon. Estuaries provide important habitat for anadromous salmonids, but the role of the Navarro River estuarine ecosystem as salmonid habitat was not known. The estuary study was part of The Navarro River Watershed Restoration Plan. Funds for the study were provided by a grant from the Northwest Emergency Assistance Program and administered by the Humboldt County Resource Conservation District. The study documents the seasonal distribution and abundance of steelhead and coho salmon in the Navarro River estuary/lagoon.

This report presents the results from field investigations of fisheries resources, and monitoring of environmental factors that act upon the estuarine ecosystem.

1. To investigate the role of the Navarro river estuary as habitat for steelhead trout and coho salmon;
2. Determine environmental factors influencing fish abundance and distribution; and
3. Use the information obtained from the field studies for fisheries and habitat assesments and making recommendations for conservation and restoration aimed at protecting or improving physical eonditions in the estuary.

We monitored water temperature, salinity, and dissolved oxygen and sampled fish populations at eleven sites in the lower three miles of the estuary from May 20, 1996 to December 3, 1997. Fish were sampled by beach seine, gill net, and hook and line. Reconnaissance level snorkel surveys provided suplementary data. Transects were established at the sampling sites for surveying cross sectional profiles of bottom topography, to characterize substrate composition, and to monitor bed load movement.

Results from the field investigations show juvenile steelhead were the most abundant fish captured and they used portions of the estuary/lagoon year round. Abundance and distribution of steelhead were influenced by seasonal downstream migrations, water temperature, salinity, dissolved oxygen levels, and channel morphology. The largest numbers of steelhead were captured May to November during both the 1996 and 1997 surveys. Steelhead were in better condition in 1996 than 1997 measured by body weight to body length relationships.

The majority of steelhead captured from the estuary in summer and fall were ages 1+ and 2+, although 0+ and 3+ fish were also captured. The size of the steelhead population residing in the estuary was estimated by a mark and recapture experiment after the sand bar closed the river mouth in September, 1997. The population was estimated for two size groups <150 mm fork length (FL) (mean FL=119 mm) and >150 mm FL (mean FL=177 mm). For the most part, the two groups represent age 1+ and 2+ steelhead respectively. The population estimate and 95% confidence interval (CI) for steelhead <150 mm FL was 2,921 +/- 635. The population estimate and 95% CI for steelhead >15O mm FL was 5,913 +/- 2361.

Judging from interpretation of adult and juvenile scales and the catch data, many Navarro River steelhead enter the ocean between March and May as they begin their third year of life and after spending at least one year in the estuary. Additionally, some appeared to enter the ocean in their second year and return to the river at age three. These data show that the estuary provides habitat year round for steelhead and is particularly important in summer and fall seasons when the river headwaters and tributaries typically have low stream flows and high water temperatures that may limit the carrying capacity for larger fish. Furthermore, many steelhead continue to utilize the estuary over winter months before migrating to the ocean in the spring or remain in the estuary another year.

Out-migrating coho salmon smolts were captured from the Navarro River estuary during May, June, and July in both 1996 and 1997. All but two coho smolts were captured from the lower estuary area. A total of ten coho smolts was captured in 1996 (mean FL=133 mm) and forty-eight were captured in 1997 (mean FL=118). The catch per beach seine for coho for similar time periods (May 21 to July 15) for both years was 0.36 for 1996 and 1.04 for 1997. The relatively small numbers of coho smolts captured from the estuary probably reflects their low abundance in the river system. The estuary, however, is important for coho smolts both as a transitional area between freshwater and saltwater environments and as a forage area as they prepare for ocean entry. The importance of estuarine rearing should not be underestimated for these fish. This is supported by the fact that coho smolts were present in the estuary until July during both years.

Water temperature, salinity, and dissolved oxygen are important environmental factors influencing the estuarine ecosystem and salmonid production. These water quality parameters are affected by interactions between several factors including freshwater flows, ocean tides, circulation and mixing pattems, channel morphology, weather conditions, and sand bar formation closing the river mouth.

The most critical factor affecting estuarine water quality and the fishery is the formation of a sand bar which typically closes the river mouth in late summer or early fall forming a lagoon. With the loss of tidal exchange, circulation of mid-water and bottom water diminishes, and stratification between low salinity or freshwater and saline estuarine water masses predominates in deep portions of the channel.

The combination of poor water circulation and salinity stratification results in solar radiation passing throuth the relatively freshwater surface layer and being absorbed by the middle and bottom saline water layer. This results in a warm water condition known as seasonal meromixis or inverse temperature stratification. On November 6, 1996, temperature in the lower water column was as much as 11°C higher than surface temperature (11°C vs 22°C) in the upper estuary.

Meromixis was observed again in September, 1997 when mid-water and lower water column temperatures reached 30°C compared to 21°C on the surface. In addition, critically low dissolved oxygen levels ( 1-3 mg/l) and anaerobic conditions also occurred in mid-water and bottom water as a result of poor circulation, and stratification. The timing and duration of lagoon formation varied between the two years of the study and is related to river flow regimes.

Steelhead avoid poor water quality in the lagoon by residing in the surface and nearshore waters and by moving upstream. Under lagoon conditions, freshwater inflows from upstream become particularly important because inflows deliver relatively cool and oxygenated water to the lagoon. The amount of suitable salmonid habitat increases as river flows accumulate in the lagoon, raising the water surface elevation, and displacing warm, anoxic saline water.

The final objective for this study was to identify areas for habitat improvements that will benefit the estuarine ecosystem and salmonid production. In my opinion, the Navarro River estuary is in a state of recovery from events that occurred in the late 1800's and early 1900's. However, excessive sediments may be accumulating in portions of the estuary and the amount of large wood present may be less than in the pre-settlement era. Unlike many estuarine systems on the West Coast, the Navarro River estuary is relatively isolated from industrial, commercial, and agricultural uses. Therefore, the area has retained much of its natural form and function.

Areas in the estuary that may be protected from erosion and slumping of banks by planting riparian vegetation and placement of woody debris include the east tip of the island and along the south channel bank just below the Highway 1 Bridge. The north bank at road marker 1.62 of Highway 128 has a problem with undercutting of the bank, willows may not be rooting through geotextile material, and rip rap is begining to fall into the channel. Additional studies are needed to determine if water quality can be improved in the lagoon. Yearly surveys of channel cross sections will provide data describing bathymetry and sediment characteristics. Further studies of the slough channels and wetlands located along the flats near the Highway 1 Bridge may reveal potential for habitat restoration. Unfortunately, road work conducted on Highway 1 south of the bridge resulted in sliding of soils across the beach access road during early fall rains. Much of the soil may end up in the wetland.

The estuary and wetlands are unique in character and considered rare habitat in California. The area is vulnerable to current and future land and water use practices in the watershed that potentially threaten the integrity of the estuarine ecosytem. Excessive accumulation of sediments in the estuary would reduce the tidal prism and probably contribute to early formation of the sand bar across the river mouth. Stabilizing upstream hill slopes and reducing upstream water temperatures by restoring the riparian corridor along the river and tributaries will indirectly benefit the estuary/lagoon. A water management plan should be developed to coordinate water diversions that considers estuarine water quality, all life history stages of coho salmon and steelhead, and hydrologic processes.

The information in this report provides the rationale for protecting the Navarro River estuary-lagoon because the estuarine ecosystem plays an important role as salmonid habitat. However, there are other fish and invertebrate species that depend on the estuary for spawning and juvenile rearing ground e.g. Pacific herring (Clupea harengus), top smelt (Atherinops affinis), shiner surf perch Cymatogaster aggregata, starry flounder (Platyichthys stellatus), English sole (Pleuronichthys vetulus), dungeness crab (Cancer magister). Under lagoon conditions, demersal species e.g. flounder, sole and crab die because of the warm, anoxic water. The estuary-lagoon should be managed to support and maintain all components ofthe estuarine ecosystem.