Freshwater ecosystems are facing a biodiversity crisis due in part to a suite of anthropogenic threats and exacerbated by changing climates. To mitigate biodiversity loss, conservation managers are tasked with distributing limited resources. Limited resources suggest the importance of geographic prioritization of conservation-related activities. Understanding biotic distributions under current and future climates can aid in identifying areas for protecting biodiversity. We assessed the distribution of freshwater mussel (12), fish (53), and turtle (1) species across six Northeastern states (Connecticut, Maine, Massachusetts, New Hampshire, Rhode Island, and Vermont). For each of the three taxonomic groups, we created habitat suitability maps using survey data and corresponding geographic, climatic, and land use data (or, in the case of wood turtle, used published maps), and we identified groups of species that were most vulnerable to changing temperature and streamflow. For freshwater mussels, we identified watersheds as high priority for land protection based on greater overall species richness, higher percent forest and wetland cover in the watershed, and higher climate resilience. For fishes, the novel biodiversity groups had different distributions than traditionally-used species guilds (temperature guilds, habitat guilds) and may offer a novel approach for identifying vulnerable species. Forest cover throughout the watershed was critical for sustaining freshwater fish and mussel species that are vulnerable to climate change. In general, watersheds with highest richness of sensitive mussels, proportional abundance of native fishes, and prevalence of wood turtles were non-overlapping, suggesting that efforts to support one group may not be sufficient to benefit all taxa, limiting the usefulness of umbrella species in this region. The broad-scale species distribution maps can be used by managers to identify watersheds for developing more focused, site-specific management actions.