Extensive urbanization impairs biological communities through landscape alteration and physiochemical changes to stream ecosystems. Analogous to urban development in cities, new building and facility expansion on university campuses can lead to dramatic changes in impervious cover and consequently, increased stormflow impacting downstream ecological communities. Here, we analyze the extent and relevance on a nationwide scale to determine campuses with the highest risk for ecological impairment. From the US‐wide analysis of 5761 college/university campuses, ~45% of campuses were within critical aquatic species watersheds, and >5% were identified as buffering critical habitat. The highest risk campus our study identified was selected to compare the impacts of planned, conventional development versus sustainable development on a sensitive aquatic species, the federally threatened Jollyville Plateau salamander (Eurycea tonkawae). Impervious cover, simulated increases in stormwater runoff, and total suspended solids (TSS) from the conventional expansion is estimated to lower salamander density. Conversely, an alternative campus expansion plan allowed for increased development but permitted provisions for reduced runoff and TSS, thereby maintaining current salamander densities. Our findings show that sustainable campus development plans have the potential to mitigate ecological disruption within watersheds, and that campus management and policies are critical for preserving biodiversity in the future.