The Severn River, Australia, is regulated by a large dam which reduces the magnitude of high flow events. Environmental flows (EFs) have been allocated to increase the magnitude of flows to improve ecological outcomes such as reducing filamentous algal biomass and re-setting succession to early stage communities. Benthic algal biomass and assemblage structure were examined at two cobble dominated riffle sites downstream of the dam before and after two EFs. Both EFs had discharges of ~11.6 m3s-1 (near bed flow velocity of ~0.9 m s-1). Neither EF reduced benthic algal biomass (as chlorophyll a) but sometimes led to increases with some filamentous algae (Stigeoclonium and Leptolyngbya) increasing in density. An unregulated flow event from a tributary between the two sites increased discharge to 25.2 m3s-1 (flow velocity of ~1.2 m s-1) which decreased biomass and filamentous algal density. The similarity in flow velocities between scouring and non-scouring events suggests that thresholds may exist and/or suspended sediments carried from unregulated tributary flows may contribute to reduce filamentous algal biomass. As EFs are becoming more widespread, target velocities to reduce filamentous algae biomass are useful. EFs with flow velocities ~1.2 m s-1 may achieve this in river cobble dominated riffle sections dominated by filamentous algae. Lower flow velocities <0.9 m s-1 may result in no change or an increase in filamentous algae.