Stoneflies (Plecoptera) are often associated with inhabiting cold perennial streams, but many species also inhabit intermittent streams that experience reduced or lack of flow during summer and autumn. In this study, the influence of stream permanence on stonefly assemblage composition and spatial distribution at Mammoth Cave National Park, Kentucky, USA, was addressed, based on a 14 month sampling regime from the fullest range of stream sizes and habitable flow regions available. Adult stoneflies were collected monthly from 43 sites at the Park plus an additional two sites at the near-adjacent Western Kentucky University Green River Preserve. Collections were done from December 2018–November 2019 using a standard timed protocol with beating sheets for adults and once in December 2019–January 2020 for larvae. Stream sites were assigned one of five category types: perennial spring runs, perennial spring seeps, upland perennial streams, perennial riverine and summer dry runs. In total, 34 species were collected. The most prominent difference in stonefly community structure was between spring runs, spring seeps and summer dry streams vs. upland perennial streams. Approximately 88% of species collected had univoltine-fast life cycles and 79% likely had an extended period of egg or larval diapause. Due to the predominance of small upland perennial and summer dry streams, species commonly typically found in larger lotic systems are fundamentally filtered out of the region due to the lack of available habitats. Species able to survive in intermittent habitats do so by life history adaptations including to survive desiccation as larvae or eggs.