Dispersal ability is an important trait that influences an organism's capability to move between populations, track optimal habitat conditions, and withstand disturbances. Aquatic invertebrates possess a wide range of dispersal abilities due to their complex life histories, multiple modes of dispersal, and high taxonomic diversity, although direct observations of dispersal is difficult for many taxa. Most community-wide analyses rely on trait databases for estimates of dispersal capability for taxonomic groups. Dispersal in individual species can be quantified using the genetic relationships between populations because dispersal is necessary for gene flow while isolation is necessary for genetic drift, but conventional landscape genetic methods are difficult to scale to multiple species. Using the ability of environmental DNA (eDNA) metabarcoding to simultaneously analyze genetic sequences from hundreds of taxa, we recovered intraspecific haplotype variation from aquatic invertebrate taxa in Grand Canyon and applied an isolation-by-distance framework to quantify dispersal ability by comparing the relative importance of gene flow and genetic drift. In total, we identified 1,201 haplotypes across 548 taxa, with 232 taxa containing sufficient genetic variability to perform landscape genetic analyses. We identified 13 taxa with high dispersal ability, 17 with moderate dispersal ability across hydrological pathways, 33 with moderate dispersal across terrestrial pathways, and 76 with low dispersal ability. The high prevalence of poor dispersers suggests widespread genetic isolation of aquatic invertebrates in the Grand Canyon, particularly between geographically isolated tributaries. Furthermore, 10 genera contained taxa that were classified to multiple dispersal abilities, highlighting how metagenetic analyses can characterize traits at a finer taxonomic resolution than conventional trait databases. By combining genetic inferences at the landscape scale with the wide taxonomic coverage of eDNA, this approach allows for simultaneous quantification of dispersal traits and enables a stronger understanding of how landscape structures metacommunities at inter- and intra-specific levels.