Abstract. The objective of the present study was to investigate the importance of emergent macrophytes as refugia in lakes of different trophic status. Furthermore, the effect of water quality on diel changes in the distribution of littoral cladocerans was of interest, with special attention paid on diurnal fluctuations of filter feeder communities, induced by pH changes under a heavy phytoplankton bloom. The study was conducted by investigating littoral cladoceran populations in different zones (inside, at the edge and outside the macrophyte stands) in two basins with divergent water quality. No tendency towards diurnal migration related to emergent macrophytes was observed in the clear-water, mesotrophic Isontalonselk basin. The dominating cladoceran, Daphnia spp., formed highest densities during daytime in the outer zone. Meanwhile, strong nocturnal cladoceran density peaks in all zones, simultaneous with lowered pH, were witnessed in the very turbid, hypertrophic Kirkkojrvi basin. Reverse horizontal migration was observed in large-bodied filter feeders, Limnosida frontosa and Sida crystallina, conceivably due to predation avoidance from young-of-the-year fish aggregating within the vegetation during the day.