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Stream and lake fishes are important economic and recreational resources that respond to alterations in their surrounding watersheds and serve as indicators of ecological stressors on aquatic ecosystems. Research suggests that fish species diversity is largely influenced by surface water connectivity, or the lack thereof; however, few studies consider freshwater connections and their effect on both lake and stream fish communities across broad spatial extents. We used fish data from 559 lakes and 854 streams from the midwestern–northeastern United States to examine the role of surface water connectivity on fish species richness and community composition. We found that although lakes and streams share many species, connectivity had a positive effect on species richness across lakes and streams and helped explain species composition. Taking an integrated approach that includes both lake and stream fish communities and connectivity among freshwaters helps inform scientific understanding of what drives variation in fish species diversity at broad spatial scales and can help managers who are faced with planning for state-, regional-, or national-scale monitoring and restoration.