Understanding how land use and variability of the hydrological regime jointly shape species distributions is essential for the conservation of aquatic insects in increasingly intermittent streams. We investigated how flow intermittency influences the relationship between land use and the occurrence probability of Cordulegaster heros in a drying river network. Field surveys were conducted at 42 stream sites in southwestern Hungary over a two-year period. We combined species presence–absence data with land use variables and hydrological proxies. Statistical analyses included decision tree modeling and binomial generalized linear models. C. heros was associated with forested landscapes and absent from sites with prolonged zero-flow periods or high agricultural land use. Occurrence probability declined markedly when forest cover was low or when dry periods were extended in duration. Although C. heros larvae can tolerate short-term drying by burrowing into sediments, prolonged flow intermittency and reduced landscape connectivity may limit both survival and recolonization. Our findings underscore the need for conservation strategies that jointly address land use and hydrological conditions to counter the rising flow intermittency expected with ongoing climate change.