At 6 sites in 5 mesotrophic softwater lakes in the wetland Zwart Water (Belgium), periphyton samples were collected on different substrates ranging from macrophytes to mosses and sandy sediment. Significant differences between substrates were observed at 5 out of 6 sites studied. The differences between the substrates, however, could not be related to known effects of these substrates on their chemical environment (e.g., excretion of H+ ions, CO2 or allelopatic substances) nor to their morphology. Therefore, differences between substrates were probably related to differences in local environmental conditions associated with these substrates. Differences in desmid community composition between substrates within a lake were always smaller than differences with samples from other lakes.