Water use for irrigation and power generation can cause fluctuating water levels in rivers. The resulting wet-dry zone is a harsh environment. We investigated tolerance to aerial exposure of cyanobacterial and green filamentous dominated assemblages in a river below a hydropower dam in northern Thailand. Rocks with algal assemblages were exposed at night, day, continuously, or were completely submerged. Day exposure was in sun or shade, and received ‘rain’ or not.  After two days, cyanobacterial biomass (chlorophyll) was greater with nighttime and continuous exposure than with day exposure. Rain and shade had minor effects. Filamentous green algal assemblages showed a strikingly different pattern. Biomass of all treatments decreased during the experiment, primarily because of snail grazing. Grazing was especially intense during the day because hydropower-related water release at night increased flow and restricted nighttime grazing. Filamentous algae exposed continuously or during the day (protected from daytime snail grazing) had greater biomass than assemblages continuously submerged or exposed at night (exposed to daytime snail grazing). We concluded that daytime aerial exposure or frequent exposure increase loss of cyanobacteria, and that interaction among grazers, hydraulic conditions, and grazer-susceptible algae is an important consideration in rivers with fluctuating flow.