AbstractDiverse macrovegetation can provide heterogeneous habitats for benthic diatoms. The removal of macrophytes as direct plant control, however, can be considered as a threat, which can even lead to remarkable microhabitat alterations. Lake Tisza (Hungary) has a high nature conservation value, but it is also an important recreation centre, which is why very delicate water management is necessary including vegetation thinning. Here, we studied the importance of microhabitat heterogeneity (emergent, submerged and floating macrophytes) in maintaining diverse periphytic diatom assemblages. We hypothesized that the substrate type has greater influencing role on the composition and diversity of diatoms than the lake heterogeneity related to basins. We also assumed that floating vegetation hosts the most different and least diverse diatom assemblages. Our results mostly proved these hypotheses. Heterogeneous assemblages were formed on the different substrates (support hypothesis), however, the basin level differences were also detected (reject hypothesis). Our results also highlighted, that macrophyte species with lesser morphological complexity hosted the least diverse periphytic assemblages (support hypothesis). However, many unique and red list taxa were found on floating plants (reject hypothesis). These findings emphasize the key role of microhabitat complexity in maintaining diverse and healthy functioning of microbial assemblages in a multi-purpose reservoir.