Historical logging practices, particularly widespread clear-cutting, caused severe erosion, which led to excessive sediment buildup in the river and its tributaries.

[4] In 1998, the river was listed as sediment impaired by the State of California North Coast Regional Water Quality Control Board.

Jackson Demonstration State Forest, owned by the California Department of Forestry and Fire Protection, makes up about one fifth of the watershed.

[7] Non-salmonid species in the watershed include the three-spined stickleback (Gasterosteus aculeatus), Pacific lamprey (Lampetra tridentata), and sculpin (Cottus spp.).

[8] Birds of special concern include the marbled murrelet (Brachyramphus marmoratus) and northern spotted owl (Strix occidentalis caurina) because of their close association with old- growth and mature redwood forest, which has been heavily impacted by timber harvest since the late 19th century.

Eighty-two mammal species are predicted to be found in the Noyo River watershed including several rodents, bats, and squirrels, beaver (Castor canadensis), black bear (Ursus americanus), ring-tailed cat (Bassariscus astutus), American marten (Martes americana), fisher (Martes pennanti), weasels, American badger (Taxidea taxus), western spotted skunk (Spilogale gracilis) and striped skunk (Mephitis mephitis), mountain lion (Puma concolor), bobcat (Lynx rufus), seals and sea lions, mule deer (Odocoileus hemionus), and elk (Cervus elaphus).