The relative importance of environmental filtering and dispersal in structuring metacommunities of littoral periphytic diatoms was assessed within a large lake (Lake Ladoga, north-western Russia). We hypothesized that different diatom functional guilds (high-profile, low-profile, motile and planktic) would respond differently to environmental and spatial variables, depending on their mode of attachment and dispersal ability. Guilds showed distinct distributional patterns along a gradient of wave-induced disturbance: low-profile diatoms dominated in exposed shorelines (high disturbance), whereas high-profile and motile diatoms were more abundant in coastal wetlands (low disturbance). Redundancy analysis with variation partitioning of the entire diatom community revealed that environmental variables (littoral geomorphology and water chemistry) outperformed spatial variables, indicating a predominant role of species sorting. When the diatom community was deconstructed into functional groups, benthic guilds (i.e., low-profile, high-profile and motile) showed higher dependence on environmental factors, whereas the planktic guild was primarily predicted by spatial factors. Thus, benthic taxa with lower dispersal abilities were less impacted by mass effects than planktic taxa. Among benthic guilds, motile diatoms were less sensitive to water chemistry compared to low-profile and high-profile diatoms, suggesting that a group-specific habitat preference may interfere with diatom responses to water quality changes. Hence, the response of diatom guilds to water quality parameters was related to their resistance to wave action. Overall, we concluded that the higher importance of environmental filtering than dispersal-related processes in shaping the diatom metacommunity resulted from a combination of a strong environmental gradient in geomorphology/water chemistry and the intermediate spatial scale of our study.