The Oneonta Tidal Linkage was constructed in the northern arm of the estuary in winter 1997. The primary goal of the project was to improve tidal circulation by connecting the northern end of Oneonta Slough with a series of isolated tidal lagoons. Both areas had been accumulating sediment as a result of dampened tidal flow.

The project consisted of a two-acre (18,000 cubic yard) excavation of disturbed upland habitat situated between the two tidal areas. The restoration quickly achieved its success criteria and now supports functioning salt marsh and intertidal habitats. A pair of endangered light-footed clapper rails has been sighted frequently in the restored area and numerous fish and invertebrate species inhabit the channel.

The Tidal Linkage Project includes a research component where scientists from the Pacific Estuarine Research Laboratory (PERL) at San Diego State University continue to investigate restoration issues.