Fires and river regulation are disturbances affecting many aquatic ecosystems worldwide. We examined the ecological response of rivers to the combined effects of regulation and fire. Changes in communities of benthic aquatic algae and macroinvertebrates were studied for 22 months following a wildfire through forested catchments in the Australian Capital Territory. In both the regulated (by dams) and the free-flowing rivers and streams, fire caused large changes to physical habitat for the benthic communities that overrode the effects of regulation. In unregulated streams, the benthic communities had largely recovered 22 months after the fire disturbance, but the regulated stream did not recover. It is not clear from the findings of this study if the benthic communities will recover from the fire disturbance without active restoration of stream habitat.