In the mid-1850s A.D. Elkhorn Slough was a minor tributary to the much larger Pajaro-Salinas River system which shared a common entrance to the Pacific Ocean north of Moss Landing.

Construction of jetties at the Moss Landing Harbor in 1946 provided a direct link between the Pacific Ocean and Elkhorn Slough.

At this time, salt marshes began to retreat from the axis of Elkhorn Slough as it evolved into its present form as a relatively stable estuarine embayment.

[6] 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.

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.

[10] 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.

The weir or "sill" is intended to reduce the excess erosion of the marsh caused by the dredging of the Moss Landing Harbor and the redirection of the Salinas River.

Similar studies in marine protected areas located off of the Santa Barbara Channel Islands have already detected gradual improvements in fish size and number.

The nonprofit Nature Conservancy was the first to buy Elkhorn Slough property with the goal to protect the area's habitat and wildlife.

It includes the waters below mean high tide within Elkhorn Slough: The SMR and the SMCA were both established in September 2007 by the California Department of Fish and Wildlife (CA−DFW).

The Moro Cojo Slough State Marine Reserve just south of Elkhorn protects a similar wetland area.

The California Office of Environmental Health Hazard Assessment has issued a safe advisory for any fish caught in Elkhorn Slough due to elevated levels of mercury and PCBs.