Influence of extreme flows on habitat and fish assemblage structure in groundwater-dominated systems

Background Periods of extreme flow ( i.e ., drought and flood) structure aquatic communities, but their effects in hydrologically stable, groundwater-dominated systems ( e.g ., karst springs) remain poorly understood. These spring systems are often viewed as refugia for endemic fishes. As such, the effects of drought and flooding are thought to be more pronounced than in hydrologically variable systems with the potential to lead to extirpations of endemic fishes. Methods We analyzed a 9-year dataset (2014–2022) from three reaches of the San Marcos River and four reaches of the Comal River, Texas, to evaluate how a major flood and a severe drought influenced habitat structure and fish assemblages among wadeable and non-wadeable areas. Habitat variables were surveyed alongside standardized fish sampling, and fishes were grouped into habitat usage guilds for analysis. Results Effects of extreme flow periods were similar to the effects reported for hydrologically variable systems in wadeable areas but not in non-wadeable areas. Among wadeable areas, an increase in the amount of algae was detected during drought, but changes to substrates and vegetation coverage because of scouring were not detected following a flood. Also, abundances of pelagic generalist fishes ( e.g ., Lepomis sp., Herichthys cyanoguttatus ) and one species of a pelagic specialist fish ( i.e ., Astyanax argentatus ) decreased following a flood. Unexpectedly, abundances of benthic guild fishes ( i.e ., Etheostoma sp.) increased during drought and abundances of one species of pelagic specialist fish ( Dionda nigrotaeniata ) decreased following a flood. Conclusions Effects of extreme flow periods on habitat structure and fish assemblages in hydrologically stable systems were similar to, or unexpectedly less pronounced, than the effects of flow periods on hydrologically variable systems. These patterns reveal vulnerabilities among generalist species during high flows and drought-associated increases for benthic taxa. These results support ecological theory that groundwater-dominated systems provide resistance to climatic extremes but remain susceptible to community restructuring, with implications for conservation under future climate variability and groundwater extraction.