Investigations of genetic structure, or genetic variation within and among populations, offer insights into ecological and evolutionary processes in freshwater ecosystems and beyond. However, there exists no framework to organize our understanding of how the spatial scales at which genetic structure is detected may vary with biological and environmental factors. This limits the transferability and generality of findings from one area to another. In our study, we investigated the spatial scale at which population genetic structure is detected for freshwater invertebrates and how this was mediated by species traits, including dispersal (mode and strength), longevity (lifespan and voltinism), and reproduction (mode and fecundity). We hypothesized that dispersal, a key driver of gene flow, would most strongly influence the scale at which genetic structure is detected, but that longevity and reproduction may be important for poor dispersers or if dispersal potential is reduced by low habitat connectivity. First, we conducted a systematic literature review to obtain > 35 microsatellite datasets for freshwater invertebrates located across four continents. We calculated FST’, a standardized measure of genetic differentiation, for all population pairs per dataset. We then tested for isolation-by-distance using Mantel correlograms to relate pairwise FST’ to pairwise Euclidean and river network distances. Trait data have been compiled for all species, and analyses to quantify the effect of traits on observed genetic structure are ongoing. Identifying how species traits may mediate the effects of spatial scale helps inform how genetic diversity is structured, particularly for freshwater invertebrates that exist in a mosaic of dendritic networks and isolated waterbodies. The framework implemented here can be used to predict genetic structure and diversity for other populations and guide future freshwater biodiversity conservation efforts.