In 1977, developers were planning an elaborate residential marina in the Tijuana River estuary in Imperial Beach, California. To protect this critical habitat, local environmental activists initiated a grassroots movement to stop the marina development. In 1979 this group formed the Southwest Wetlands Interpretive Association (SWIA), a non-profit 501(c)3. Working cooperatively with the U.S. Navy and the U.S. Fish & Wildlife Service (USFWS), the marina development was blocked and the estuary spared. In 1980 the 505-acre Tijuana Slough National Wildlife Refuge was created to permanently protect endangered and threatened species that depend on the estuary and salt-marsh habitat. In 1982 the National Oceanic and Atmospheric Administration (NOAA) extended federal protection with the creation of the 2800-acre Tijuana River National Estuarine Sanctuary. The Sanctuary, now known as the Tijuana River National Estuarine Research Reserve (TRNERR), contains the Refuge and other public and private land.

In 1990 SWIA, together with California State Parks (CSP), USFWS and NOAA, constructed the award-winning, $1.2 million Tijuana Estuary Visitor Center at the northern end of the Tijuana River National Estuarine Research Reserve (TRNERR). In 1992 SWIA was project manager for Ecoparque, an innovative, low tech wastewater recycling project in Mexico. This binational project addressed sewage overflow issues at the border and was funded through the State Coastal Conservancy.

Over the years SWIA has managed cutting edge wetlands restoration projects throughout the Tijuana River Valley. In 1992 the Tijuana NERR Management Authority adopted the Tijuana Estuary Tidal Restoration Program (TETRP) that calls for the restoration of 520 acres of inter-tidal wetlands. TETRP is one of the largest wetlands restoration projects in the nation. In 1997 SWIA managed the first phase of this plan, the Oneonta Tidal Linkage project, which enhanced circulation and increased tidal flushing in 200 acres of intertidal salt marsh. In 1999 SWIA managed the next phase of TETRP, the Model Marsh Project. Through excavation, re-vegetation and natural species colonization this project created a twenty acre intertidal marsh plain with both mudflat and vegetated areas. SWIA is currently the project manager for TETRP II, which is in the process of developing a restoration plan based on Model Marsh research findings for the remainder of the target wetlands. SWIA is currently partnering with the State Coastal Conservancy and United States Fish & Wildlife Service to develop a program to eradicate and control invasive non-native plants in both public and private lands in the Tijuana River Valley.