Riverine ecosystems are profoundly influenced by hydrological dynamics and natural flow regimes, which dictate the temporal variability of water levels and the amplitude of fluctuations. Human activities, particularly navigation and hydropower generation, have significantly altered these natural patterns, leading to detrimental impacts on the physical, chemical, and biological integrity of river ecosystems. The littoral zone, in particular, is highly susceptible to anthropogenic disturbances, experiencing disruptions in biological activity and biogeochemical processes. This study evaluates the effects of ship-induced wave trains on the structural and functional properties of periphytic algal communities in a regulated river environment. Using data from the Austrian Danube River, periphytic algae's immediate and long-term responses to wave events generated by different types of ships were investigated. Immediate reactions of periphytic algae to wave trains were characterized by reductions in the effective quantum yield of PS II, indicating stress-induced down-regulation of photosystem II photochemistry. Abrasion and remobilization of periphytic algae due to wave action led to increased resuspension of chlorophyll-a into the water column. Furthermore, ship-induced wave trains influenced the pigment composition of periphyton, with photoprotective mechanisms being activated in response to fluctuating light conditions. Long-term effects of wave impact on periphytic algae biomass varied depending on water depth and exposure to aerial stress. While wave action mitigated desiccation stress in shallow areas, it resulted in biomass reduction and alterations in community composition in deeper zones. Notably, the occurrence of diatoms decreased in wave-impacted areas, potentially shifting the community towards Chlorophyceae dominance. Overall, this study underscores the complexity of ship-induced wave impacts on riverine ecosystems and highlights the importance of considering both immediate and long-term responses of periphytic algal communities. Understanding these dynamics is crucial for informing sustainable management strategies aimed at mitigating the adverse effects of navigation activities on riverine biodiversity and ecosystem functioning.