Biodiversity across levels of biological organization, from genes to communities to ecosystems, is responding to rapid environmental change globally. Yet the degree to which diversity at different biological scales responds to environmental drivers in parallel or in divergent ways remains poorly understood and difficult to predict. This is true for benthic organisms affected by stream drying, a phenomenon increasing in frequency and severity globally. Despite advances in understanding how stream drying independently influences species diversity and genetic diversity of aquatic organisms, whether species and genetic diversity are responding in parallel ways to stream drying dynamics remains unclear. For example, does high species diversity always correlate with high genetic diversity? Or, does the relationship between species and genetic diversity depend on environmental or biological factors? As part of the StreamCLIMES Project, we tested species-genetic diversity correlations (SGDCs) for multiple macroinvertebrate taxa in five stream basins across the southern United States. We generated population genetic datasets (COI and double-digest restriction-site associated DNA) for focal mayfly taxa (Baetidae/Caenidae) from each stream basin for comparison with macroinvertebrate community surveys. We hypothesized that the strength and direction of SGDCs vary among basins and taxa, and that a combination of biological (trait-based) and environmental (landscape, flow permanence) factors explain the strength and direction of observed SGDCs. We present findings from a weighted, information-based decomposition framework to compare levels of allelic and species diversity. Overall, our study helps inform when positive SGDCs can be expected in stream ecosystems and the role that stream drying plays. This is particularly vital when conservation and research resources prohibit genetic analysis for all species of interest, in which cases community-level data may serve as a proxy for population-level biodiversity.