We use multiple years of collections in rivers, perennial wetlands, and ephemeral tinajas to report on overall biodiversity of aquatic invertebrates in the Grand Staircase–Escalante National Monument, Utah. A total of 570 samples of aquatic invertebrates was collected at 166 locations. Over the study period, invertebrates were identified from 31 orders, 104 families, and 192 genera. Major habitat types (rivers, perennial wetlands, and ephemeral tinajas) supported unique and taxonomically rich assemblages of invertebrates; taxonomic richness was greatest in rivers. Among rivers, richness of genera of aquatic invertebrates was greatest in groundwater-fed streams and perennial, snowmelt-runoff, rivers and least in flood-prone rivers. Future studies should focus on identifying and collecting invertebrates from unique habitats, especially the numerous wetland-like habitats that occur across the Grand Staircase–Escalante National Monument, such as hanging gardens and alcove pools, as well as ephemeral streams.