Physical disturbance owing to spates can have a significant influence on the structure and dynamics of periphyton assemblages in streams. The effects of flooding on epilithic algae in two subtropical rainforest streams was investigated. Periphyton chlorophyll a and biomass (mainly of diatom origin) were monitored over three and a half years in relation to rainfall and stream discharge. High discharge events had a reducing effect on periphyton chlorophyll a and biomass in both streams. However, these values recovered quickly (within a period of approximately 10–30 days post-spate) in the absence of any further disturbance. After approximately 60 days, however, levels declined in the absence of subsequent disturbances. Differences in the epilithon between the two streams could be related to the geomorphology and the pattern of disturbance. Cobbles in the steeper-gradient stream-reach supported more chlorophyll a containing material of algal origin and less non-algal biomass than those in the low-gradient stream-reach. Overall, changes in the standing crop of epilithic algae could be attributed directly to the effects of spates. However, some major variations in chlorophyll a and biomass occurred in the absence of high discharge events, suggesting that other factors, such as extreme low flows, could also be significant agents of disturbance.