The second phase of the Tijuana Estuary Tidal Restoration Program (TETRP), the 20-acre Model Marsh Project, was constructed in an area of former salt marsh that was filled through a series of natural and man-induced events. The project involved the excavation of approximately 100,000 cubic yards of soil to create a marsh plain with a network of tidal channels.

Although the marsh plain surface is relatively flat, (1% slope), it was constructed with the goal of creating three habitat types: the area lowest in elevation located near the main intertidal channel was designed to function as mudflat; a middle elevational band of marsh plain was planted with Pacific cordgrass to encourage development of the preferred breeding habitat of the endangered light-foot clapper rail; and the highest marsh plain elevation were left unplanted to develop salt marsh via natural recruitment.

Like the Tidal Linkage project, the Model Marsh includes an extensive research program, with research conducted by PERL and the Scripps Institution of Oceanography, University of California, San Diego. A primary research focus is to test the role of tidal creeks in the development of wetland habitats.