The Júcar River Basin (Spain) harbours endemic aquatic species that are declining or going extinct at an alarming rate. After evaluating several possible stressors, flow modification is identified as the factor critically threatening one endemic cyprinid fish species Chondrostoma arrigonis. Physical habitat for this species is compared for river reaches with different flow modification histories to understand local extinctions across this species' historical range. Time-series of physical habitat, generated using PHABSIM, indicate a dramatic reduction in habitat area with flow modification. Our findings indicate that efforts to regulate and stabilize flows in the Júcar River Basin may cause the rapid extinction of the remaining populations.