We analyzed long-term (5-8 yr) hourly time series of chlorophyll (Chl) converted from fluorescence measurements in relation to discharge and light in three medium-to large-size rivers, where planktonic diatoms dominated during the growing season. Overall, there was an inverse relationship between discharge and Chl. At fine temporal scales, flow pulses were typically accompanied by an increase in diatom Chl. In contrast, chlorophytes were usually diluted. The increase in diatoms was likely due to resuspension of meroplanktonic species from the bottom. The benthic retention hypothesis proposes that rapidly sedimenting diatoms take advantage of a prolonged benthic residence provided that the enhanced retention is sufficient to compensate for slower light-supported growth at the bottom relative to water. This hypothesis was tested with simple growth models. Although the rivers were highly turbid and did not support net growth when flow exceeded a rather low threshold, benthic retention might have favored low-light-adapted algae during more than half of the period when net growth was possible. Among the physical factors, the rate of resuspension might be the critical factor that determines the ultimate success of a meroplanktonic life cycle strategy. The three rivers of this study rarely supported persistent planktonic populations. We propose that self-sustaining populations of riverine algae are primarily based on meroplanktonic diatom species, whereas truly planktonic populations, mostly chlorophytes, depend on periodic inoculations from out-of-channel sources.