is the primary source of freshwater flowing into Elkhorn Slough. McClusky Slough to the north and Moro Cojo Slough to the south also provide freshwater inputs.
Conservation ownership
More than of the watershed's are protected under a mosaic of private and public ownership.
Foundations
The nonprofit Elkhorn Slough Foundation is the single largest land owner in the watershed, with nearly. The nonprofit Nature Conservancy was the first to buy Elkhorn Slough property with the goal to protect the area's habitat and wildlife. The Nature Conservancy started with only 60 acres in 1971 and through gifts and purchases of disjointed parcels, gained over by September 2012, when it transferred to the Elkhorn Slough Foundation. The Foundation already managed conservation on these parcels.
The Elkhorn Slough State Marine Reserve covers. The SMR protects all marine life within its boundaries. It is managed by the California Department of Fish & Wildlife in cooperation with the National Oceanic and Atmospheric Administration. Fishing and take of all living marine resources is prohibited. It includes the waters below mean high tide within Elkhorn Slough lying:
The Elkhorn Slough National Estuarine Research Reserve is one of 28 National Estuarine Research Reserves established nationwide as field laboratories for scientific research and estuarine education.
Elkhorn Slough, one of the largest estuaries in California, provides essential habitat for over 700 species, including aquatic mammals, birds, fish, invertebrates, algae and plants. The slough area is home to California's greatest concentration of sea otters, as well as populations of endangeredSanta Cruz long-toed salamander and the threatenedCalifornia red-legged frog. The population of sea otter living in Elkhorn Slough reflect that the species is well-adapted for estuarine habitat, and may be a model for the historical sea otter populations now extinct in San Francisco Bay. Elkhorn Slough hosts year-round residents tightly associated with estuaries, such as pickleweed, eelgrass, oysters, gaper clams, and longjaw mudsuckers, as well as important seasonal visitors such as migratory shorebirds, sea otters, and sharks and rays. Habitat types include mudflats, tidal creeks and channels. Other vegetative species include such wildflowers as yellow mariposa lily, Calochortus luteus.
Restoration
Conservation groups have worked to remedy indirect harm from human activity in the region in addition to preventing direct damage to the ecosystem by harvest of resources and conversion of land.
A one million dollar grant in 2019 will restore of tidal wetlands.
Recreation
Along with hiking and bird watching, kayaking and stand-up paddle boarding are popular activities on the slough. Watching sea otters, sea lions, seals, brown pelicans, American avocets, cormorants, egrets, terns and a host of other wildlife from the water is an experience that provides a unique perspective of how the slough is used by the native inhabitants. People are encouraged to keep at least 100 feet of distance between them and wildlife on the slough. The Elkhorn Slough National Estuarine Research Reserve and Elkhorn Slough Foundation provide on-site management, education, and stewardship and offer public access via of trails, as well as a Visitor Center and volunteer opportunities. The nearby Moss Landing Wildlife Area protects of salt ponds and salt marsh. Limited recreation is permitted within the Wildlife Area. Harvest of finfish and clams are allowed within the conservation area only. Clams may only be taken on the north shore of the slough in the area adjacent to the Moss Landing State Wildlife Area. California’s marine protected areas encourage recreational and educational uses of the ocean. Activities such as kayaking, diving, snorkeling, and swimming are allowed unless otherwise restricted. The Moss Landing Harbor District has jurisdiction over the navigable waterways of Elkhorn Slough and owns Kirby Park at the upper reaches of Elkhorn Slough. Kirby park has a small boat launch and provides parking for a small trail on Nature Conservancy property at the north side. The trail here is fully handicapped-accessible and allows a walk and a wheelchair near the water's edge.
Scientific monitoring
As specified by the Marine Life Protection Act, select marine protected areas along California’s central coast are being monitored by scientists to track their effectiveness and learn more about ocean health. Similar studies in marine protected areas located off of the Santa Barbara Channel Islands have already detected gradual improvements in fish size and number.