Extreme flow events in the form of major floods and droughts are primary drivers in structuring aquatic habitats and communities. While floods and droughts can alter aquatic biota by displacement or increased mortalities, extreme flow events can have indirect and prolonged effects on by altering habitat complexity, which in turn delays recovery of the aquatic biota. Interrelationships among extreme flow events, habitat complexity, and fish assemblages are established in hydrologically variable rivers (run-off dominated). Less known are the interrelationships among stream flow extremes, habitat complexity, and fish assemblages in hydrologically stable rivers (groundwater dominated). Purpose of this study was to assess how extreme flow events affect habitat complexity and fish assemblage within two hydrologically stable rivers in Texas (San Marcos and Comal rivers).. Habitats (N = 4,863) within 12 reaches of the rivers were categorized as high, moderate, or low complexity along a depth, vegetation, substrate, and current velocity gradient. Following or during flow events, shifts in habitat complexity were not evident except in low complexity reaches that shifted towards greater complexity during drought. Among a total of 43 fish species and 135,199 individuals observed, CPUE of surface fishes (Gambusia), pelagic generalist fishes (e.g., Lepomis), pelagic specialist fishes (e.g., Dionda), and benthic fishes (Etheostoma) were generally greater in high and non-wadeable moderate complexity reaches than in lower complexity reaches and were generally unaffected by extreme flow events. Results indicated that habitat complexity in hydrologically stable rivers supports greater fish CPUE, and habitat complexity and fish assemblage were more resistant to extreme flow events in hydrologically stable rivers than in hydrologically variable rivers.