The ecological structure and distribution of diatom communities in semi-arid freshwater systems are shaped by complex interactions between hydrological regimes, physicochemical gradients, and anthropogenic pressures. This study presents the first comprehensive assessment of spatial and seasonal diatom dynamics in the Sidi Chahed Reservoir and its main tributaries (Oued Mikkes and Oued Mellah), a key freshwater resource in Morocco's semi-arid region. Sampling was conducted monthly across multiple stations from December 2022 to November 2023, capturing seasonal variations in hydrology and water quality. A total of 74 species representing 33 genera were identified, with the assemblage composition revealing marked spatiotemporal patterns. Taxa such as Nitzschia palea, Achnanthidium cf. minutissimum, and Staurosirella sp. were among the most abundant and served as indicators of organic pollution, mineralization stress, and seasonal hydrological shifts. Statistical analyses and Biological Diatom Index (BDI) results highlighted salinity as a dominant geogenic driver, with temperature, nutrients, and dissolved oxygen also shaping community structure. Notably, 16 taxa are proposed as new records for Moroccan freshwater ecosystems, underscoring the region's underexplored diatom diversity. These findings underscore the utility of diatoms as bioindicators in semi-arid reservoirs and provide a baseline for future ecological monitoring in North African freshwater systems under increasing anthropogenic and climatic pressures.