Diversity and distribution of Neotropical aquatic insects is still poorly known, with many species to be recorded and many others to be described, due to the small number of taxonomists and sparse faunistic studies. This knowledge is especially poor in the Caatinga Domain in Northeastern Brazil, even though, this region may have played an important historical role in the spatial evolution of faunas of forested areas in northern South America. Aquatic insect checklists of 96 species from Parque Nacional de Ubajara (Ceará State, Brazil) and 112 species from Parque Nacional de Sete Cidades (Piauí State, Brazil) are presented, representing the following taxa: Elmidae, Epimetopidae, Hydrophilidae, and Torridincolidae (Coleoptera), Hemerodromiinae (Diptera: Empididae), Ephemeroptera, Gerromorpha and Nepomorpha (Hemiptera), Odonata, Plecoptera, and Trichoptera. Because of the scarce number of biological inventories in Northeastern Brazil, several new distributional records (of species, genera, and families) for Brazil, Northeastern Brazil, and Ceará and Piauí states are provided. In addition, several undescribed species were detected, being 26 from Ubajara and 20 from Sete Cidades. Results represent a significant increase to the known fauna of these states, ranging from 13%-70% increase for Ceará and 41% to 91% increase for Piauí. Although both parks are relatively close to each other and within the Caatinga domain, their aquatic fauna display a very high complementarity (89% species), possibly due to structural differences of water bodies sampled in each park. Rarefaction curves based on quantitative light trap samples suggest a much higher expected species richness of aquatic insects at Sete Cidades than at Ubajara National Park. Discussion on biogeographical affinities of this sample of the Caatinga fauna is provided.