Historical accounts indicate that the Estuary Subbasin supported populations of Chinook salmon, and steelhead trout throughout the summer months, in addition to being a vital transitional step on the seaward migration of juvenile salmonids and the returning spawning migration of adult salmonids. Biological studies were conducted in the estuary in the late 1980s and early 1990s by HSU researchers and the Mattole Restoration Council along with current population counts by the Mattole Salmon Group. These studies indicate that over-summering Chinook salmon and steelhead trout populations in the Estuary Subbasin are currently depressed;
Instream sediment from both past land use and natural geologic processes upstream has been delivered to the estuary by large storm events, impacting the low gradient estuarine channel. Comparison of 1942 and 1965 photos indicates that the estuary widened, and areas of vegetation were lost during that time frame. However, the 1984 and 2000 aerial photos show some channel narrowing and vegetative improvement during this time period. Whereas dormant landslides, steep terrain and areas with high to very high landslide potential indicate that slopes in the subbasin are susceptible to landsliding and erosion, the bulk of excess instream sediment appears to have been transported from upstream sources;
Soil disturbance associated with several agricultural and development activities have exacerbated the naturally high levels of sediment delivery to the Mattole River and its tributaries. In particular, vegetation removal and road construction during the post 1950 peak timber harvest period, coupled with the transport energy of the devastating floods of 1955 and 1964 have created extensive negative stream characteristics in the lower reaches of many large tributaries including mainstem Honeydew Creek. These negative impacts include displaced riparian vegetation; wide, aggraded channels; and very warm summertime water temperatures. These impacts have become resident in the Estuary Subbasin;
The present state of estuarine habitat is limiting the successful production of salmonids, especially Chinook salmon. Based on known salmonid temperature suitability studies, current sediment, and temperature impacts in the estuary are thought to be deleterious to summer rearing salmonid populations. Results of habitat assessment conducted from 1988 through 1994 in the estuary by Humboldt State University, Mattole Restoration Council, and Mattole Salmon Group researchers identified a critical shortage of adequate pool habitat, water depth, substrate embeddedness, and escape and ambush cover. These are all necessary for survival of salmonids in the critical over-summering life stage;
Although lack of escape cover for fish increases the risk of predation by birds, mammals, etc., data from other river systems indicate that seal and sea lion predation is usually not limiting to salmonids. These data indicate pinnipeds are not likely to have a large impact on Mattole Basin salmonid runs.