Hitherto, HSI models have largely been utilized to quantify the quality of existing habitat for wildlife species, without reference to how that habitat may have been altered in the past or how it might be altered in the future. In this study, we are using HSI models as part of an integrated modeling approach to estimate the risk of habitat quality gain or loss for a variety of indicator species due to future climate change and aquifer management decisions at the San Pedro Riparian National Conservation Area (SPRNCA). Current anthropogenic stressors, including agricultural and municipal water use, are having adverse impacts on the extent and quality of riparian habitat in the SPRNCA. Future climate change, through its potential effects on hydrology and water demand by local communities, may exacerbate these effects. Because of these current and potential future changes, vertebrates that depend on riparian habitats for their breeding, wintering or migration sites are at risk. Combining climate, hydrology, and vegetation modeling with HSI models allows us to predict the effects these risks.