Many freshwater ecosystems worldwide, and particularly Mediterranean ones, show increasing levels of salinity. These changes in water conditions could affect abundance and distribution of inhabiting species as well as the provision of ecosystem services. In this study we conduct laboratory experiments using the macroinvertebrate Smicridea annulicornis as a model organism. Our factorial experiments were designed to evaluate the effects of geographical origin of organisms and salinity levels on survival and behavioral responses of caddisflies. The experimental organisms were captured from rivers belonging to three hydrological basins along a 450 Km latitudinal gradient in the Mediterranean region of Chile. Animals were exposed to three conductivity levels, from 180 to 1400 μS/cm, close to the historical averages of the source rivers. We measured the behavioral responses to experimental stimuli and the survival time. Our results showed that geographical origin shaped the behavioral and survival responses to salinity. In particular, survival and activity decreased more strongly with increasing salinity in organisms coming from more dilute waters. This suggests local adaptation to be determinant for salinity responses in this benthic invertebrate species. In the current scenario of fast temporal and spatial changes in water levels and salt concentration, the conservation of geographic intra-specific variation of aquatic species is crucial for lowering the risk of salinity-driven biodiversity loss.