The Bureau of Land Management and the USDA Forest Service manage most of the upper one-third of the watershed. The industrial timber lands are owned and managed by a handful of companies including: Green Diamond Resource Company (the largest private land owner in the watershed), Sierra Pacific Industries, and Humboldt Redwood Company. Land uses within the watershed include timber harvest, cattle ranching, agriculture, gravel mining, roads and residential development.

A number of threatened Endangered Species Act (ESA) listed fish live in the river, including: Chinook (Oncorhynchus tshawytscha) and Coho salmon (O. kisutch), summer and winter-run Steelhead (O. mykiss), Eulachon (Thaleichthys pacificus), and Longfin smelt (Spirinchus thaleichthy) are found within the Mad and its estuary. Endangered avian species found within the riparian corridor include the Willow Fly Catcher, Yellow Billed Cuco, Marbled Murrelet and the Western Spotted Owl. 

Since 1971, the California Department of Fish and Wildlife has operated the Mad River Fish Hatchery. The hatchery releases about 150,000 juvenile steelhead annually in the spring. It is also used as a rearing facility for salmonids that originate from and will be released back into other basins. The hatchery also raises rainbow trout for local put-and-take fisheries. 

The Baduwa't River estuary is recognized for protection by the California Bays and Estuaries Policy. In 1992, the Environmental Protection Agency added the Baduwa't River to the California Clean Water Act impaired water list due to elevated sedimentation/siltation and turbidity. The California North Coast Regional Water Quality Control Board (RWQCB) identified water temperature as an additional impairment to the watershed in 2006.