The Bay has four major tributaries: Jacoby Creek, Freshwater Creek, Elk River and Salmon Creek. The watersheds of each of these tributaries are predominantly industrial timberlands. Over the past twenty years, aggressive logging practices, often on very steep and highly erosive slopes, have caused tremendous amounts of sediment to enter the Bay. Freshwater, Jacoby, and Elk rivers are listed by the State Water Quality Control Board as impaired for sediment and siltation.

Although it does not appear on the 303(d) list, Salmon Creek has significant water quality problems as well. Due to agricultural activities (primarily forestry, dairies and cattle ranches) in the Salmon Creek watershed, the levels of contaminants in the creek have been high enough to make the creek a highly turbid and a foul-smelling public nuisance during summer low-flow periods.

The Humboldt Bay Watershed is entering its third decade of restoration efforts, but much work is needed to address the up-slope areas of sediment delivery. As long as clearcut logging practices remain the norm on our steep and erosive terrain, the Bay's salmonid populations will continue to suffer.

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