From the mouth, brackish waters extend 8 miles (13 km) upstream, forming the longest undeveloped estuary in the state.

Pre-European contact, the lands about the Big River belonged to the Me-tum’mah, or Mitom Pomo.

[4] Big River was named for the giant redwoods that once lined its banks; it's shown as Arroyo Grande on a diseño of the Albion Mexican land grant of October 30, 1844.

This method of log transport increased erosion, removed woody debris, and buried cobble substrates.

The river provides recreation and groundwater recharge for agricultural and industrial water use for the community of Mendocino, California.

[6] Other native fishes include the anadromous Pacific lamprey (Lampetra tridentata), sculpins (Cottus spp.

Many marine fish species also enter the estuary seasonally to feed, such as night smelt (Spirinchus starski), while a variety of coastal species pass in and out of the estuary year-round, including cabezon (Scorpaenichthys marmoratus), tidepool sculpin (Oligocottus maculosus), and kelp greenling (Hexogrammos decagrammus).

[13] Beaver ponds help restore salmonid habitat by capturing sediment and improving water quality, providing pools for juvenile salmonid over-summering, raising water tables which recharge streams in the dry season, increasing the area of aquatic and riparian habitat providing fish cover, and attenuating flashy storm flows.

[14] A recent comprehensive literature review of the effects of beaver impoundments on fish illustrates that loss of beavers was directly related to significant population declines of now threatened or endangered California salmonids, including three species listed under the Endangered Species Act: Coho salmon (Oncorhynchus kisutch) (endangered), steelhead (Oncorhynchus mykiss) (threatened) and Chinook salmon (Oncorhynchus tshawytscha) (threatened).

As with most watersheds on the northern California Coast, the most significant ecological problem in the area is increased erosion caused by logging, leading to excessive sedimentation in the river and its tributaries.

Consequestly, the Big River has been listed as sediment and temperature impaired since 2003 under section 303(d) of the Clean Water Act.