The large uncertainty surrounding the effects of sea-level rise and climate change on tidal marsh habitats and the species that depend on them exacerbates the difficulty in planning effective conservation and restoration efforts. To help conservation practitioners address these effects, we modeled the distribution and abundance of tidal marsh bird species in the San Francisco Estuary every twenty years between 2010 and 2110 in relation to projected changes in sea-level rise, salinity, and sediment availability. These distributions were projected for four future scenarios with assumptions of low or high suspended sediment concentrations and low or high rates of sea-level rise (0.52 m or 1.65 m/100 yr) to assess the sensitivity of models to uncertainty in future conditions. We used the projections of bird populations to develop spatially-based priorities for conservation and restoration using Zonation conservation planning software. We tested whether the ranking of the top 25% of proposed restoration projects changed based on which future scenario we used in the Landscape prioritization. We used the for future scenarios, one scenario only including current conditions and one scenario with all future scenarios included to rank the potential restoration projects. We found that ranking restoration projects based on current conditions consistently resulted in fewer tidal marsh birds protected under all scenarios. Ranking the restoration sites based on only one of the four available future scenarios showed variable performance. Ranking restoration projects using the “all scenarios” prioritization consistently performed as well as or better than rankings using individual scenarios. Our results demonstrate the value of using models of different scenarios when uncertainty in future conditions is high to ensure that climate change adaptation plans are robust to the uncertainty in future conditions.