Many endangered species live in extremely altered habitat and historical habitat may only be known through written descriptions of landscapes prior to alteration. Restoring habitat for species in these situations can be difficult when there are unknowns and consensus on design is needed to ensure habitat elements for listed species. California’s Central Valley is reflective of this situation where the vast expanse of wetlands has been levied and converted to agriculture and development. Lookout Slough, a large-scale multi-benefit restoration project for fish habitat and flood protection would create tidal wetland habitat reflective of historical conditions. The project provides a great opportunity to include design elements for the semi-aquatic giant gartersnake (Thamnophis gigas), a threatened species endemic to the Central Valley. The species was previously believed extirpated in the region, but detected by the project during the planning phase. Habitat design was a collaboration between species experts, agency personnel, and the project design team to incorporate both aquatic and terrestrial habitat elements for the snake while still meeting project goals for fish restoration credits. Habitat design was adjusted to reduce snake winter refugia flood risk. An overview of the project and processes to address design uncertainty for snake habitat is provided.