There has been increasing interest in algae‐based bioassessment, particularly, trait‐based approaches are increasingly suggested. However, the main drivers, especially the contribution of hydrological variables, of species composition, trait composition, and beta diversity of algae communities are less studied. To link species and trait composition to multiple factors (i.e., hydrological variables, local environmental variables, and spatial factors) that potentially control species occurrence/abundance and to determine their relative roles in shaping species composition, trait composition, and beta diversities of pelagic algae communities, samples were collected from a German lowland catchment, where a well‐proven ecohydrological modeling enabled to predict long‐term discharges at each sampling site. Both trait and species composition showed significant correlations with hydrological, environmental, and spatial variables, and variation partitioning revealed that the hydrological and local environmental variables outperformed spatial variables. A higher variation of trait composition (57.0%) than species composition (37.5%) could be explained by abiotic factors. Mantel tests showed that both species and trait‐based beta diversities were mostly related to hydrological and environmental heterogeneity with hydrological contributing more than environmental variables, while purely spatial impact was less important. Our findings revealed the relative importance of hydrological variables in shaping pelagic algae community and their spatial patterns of beta diversities, emphasizing the need to include hydrological variables in long‐term biomonitoring campaigns and biodiversity conservation or restoration. A key implication for biodiversity conservation was that maintaining the instream flow regime and keeping various habitats among rivers are of vital importance. However, further investigations at multispatial and temporal scales are greatly needed.

Rivers and related freshwater ecosystems are facing increasing natural disturbance and anthropogenic stressors. Understanding the key ecological processes that govern the riverine biota in aquatic ecosystems under multiple pressures has crucial importance. However, there is still insufficient knowledge in quantifying of stressors interactions. Moreover, the understanding of the responses of riverine phytoplankton to multiple stressors is still scarce from catchment aspect. As an interdisciplinary study, the catchment hydrological processes were linked to ecological responses in this study, and we chose phytoplankton functional groups (PFGs) instead of taxonomic classifications of algae to examine their responses to land-use pattern (L), hydrological regime (H), and physicochemical condition (P) across two contrasting hydrological periods (dry, wet). The traits-based phytoplankton functional groups are highly suggested as robust bio-indicators for better understanding the current ecological status. The hydrological regime was described by a matrix indices of hydrological alteration based on the outputs of a well-established ecohydrological model (SWAT). The results from variation partitioning analysis showed that P and H dominate during the dry period and P in high flows. Structural equation models (SEM) showed that the skewness of 7 days discharge emerged as a key driver of H, and had always an indirect effect on functional group TB (benthic diatoms) during both hydrological periods. The functional group M (mainly composed by Microcystis) has directly related to phosphorous in both periods, while indirectly to L of urban area in high flow period, and water bodies in low flow period. This study emphasized that climate change and anthropogenic activities such as altering flow regime and land-use pattern affect directly or indirectly riverine phytoplankton via physicochemical conditions. In addition, our findings

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