The San Joaquin Freshwater Marsh Reserve represents one of the last remnants of freshwater wetlands that once covered much of Orange County’s flood plain. Located in an ancient river-cut channel at the head of Newport Bay, the reserve supports a variety of wetland habitats, including freshwater marshlands, shallow ponds, and channels confined by earthen dikes. Dry upland habitats with a remnant coastal sage scrub community rise on the margins of the reserve.

RJM restored a series of the wetland riparian waterways and created valuable water quality filtering thorough the use of bio-swales and settling ponds. The Creek water is diverted into the marsh, it is then circulated through ponds for several days before being returned to the creek, about a mile upstream of Newport Bay. Few visitors to the sanctuary would guess that the plants in the ponds, and the microbes attached to them, draw nitrogen out of the water, leaving it cleaner than when it entered. The microbes release the nitrogen harmlessly into the atmosphere, which is already 79% nitrogen. After circulating through the ponds for two weeks, the cleaner water is returned to the creek with about half the nitrogen levels.

RJM's designs completely re-graded the waterways, improving spillways and flow controls, introduced decomposed granite walkways, trails, seating areas and parking.

The marsh is a critical stopping place for 100 migratory bird species using the Pacific Flyway.

Altogether, more than 200 bird species (20 nesting) have been sighted in the reserve, including two resident endangered bird species: the light-footed clapper rail (Rallus longirostris levipes) and the California least tern (Sterna albifrons).