The watershed has been logged for timber since the 19th century. Historical logging practices, particularly widespread clear-cutting, caused severe erosion, which led to excessive sediment buildup in the river and its tributaries. In addition, large woody debris that trapped sediment was removed from the streambed to improve flows. Noyo River estuary is recognized for protection by the California Bays and Estuaries Policy. In 1998, the river was listed as sediment impaired by the State of California North Coast Regional Water Quality Control Board. The watershed is slowly improving, but it is far from full recovery.