Freshwater habitats can sustain high biodiversity, but habitat degradation, species invasion, and overexploitation have imperiled freshwater species. The multiple threats to freshwater habitats and changing stream characteristics due to climate change make it challenging to identify the drivers of fish vulnerability, especially given that the importance of drivers may vary by the biodiversity endpoint. The goals of this study were to 1) describe freshwater (lotic) fish biodiversity across northeastern states in the United States, and 2) identify geographic, climate, and land use drivers of fish biodiversity, toward improving freshwater fish conservation. We predicted habitat suitability for 53 fish species using survey data and corresponding geographic, climate, and land use data. After model fitting, we grouped species using a traditional approach based on traits and a new approach using modeled streamflow and stream temperature to create clusters. We found that climate and land use vulnerable groups did not always have similar geographic patterns or relationships to the climate or land use variables, suggesting that biota vulnerable to changing conditions may be overlooked by reliance on predefined guilds to set conservation goals. Biodiversity groups that were vulnerable to climate variables were also related to land use variables that can be used to identify restoration opportunities. This approach may be useful for managers interested in holistic freshwater management under changing stream conditions.