<p>This study presents the first application of the Biological Diatom Index (BDI) in Morocco, focusing on the Sidi Chahed reservoir and its tributaries, Oued Mikkès and Oued Mellah. The objective was to evaluate whether the BDI can reliably assess ecological quality in semi-arid systems dominated by geological salinity. Monthly sampling over one hydrological year included epilithic diatoms at riverine stations and planktonic assemblages in the reservoir water column. The Biological Diatom Index (BDI) was applied exclusively to epilithic samples from riverine stations, as the index is calibrated for benthic habitats, while reservoir planktonic assemblages were analyzed to describe vertical and seasonal community structure. A total of 80 diatom species from 35 genera were identified across the entire system. Epilithic assemblages from tributaries (72 species) exhibited higher richness than planktonic assemblages from the reservoir (46 species), with clear depth-related zonation in the water column. Diatom community structure, and thus BDI performance, was primarily governed by salinity stress from Triassic evaporites, with drought-driven hydrology amplifying seasonal variability. The index revealed three distinct spatial responses: a chronically stressed saline tributary, a dilution refuge at the confluence, and a volatile agricultural tributary where summer drought caused sharp declines in ecological status. Indicator species confirmed these patterns, with <i>Nitzschia palea</i> and <i>Tryblionella hungarica</i> associated with low BDI values, while sensitive taxa prevailed under more favorable conditions. We conclude that the BDI is a robust bioassessment tool for riverine systems in semi-arid regions but must be interpreted within the local geological and climatic context. A regionally calibrated diatom index is recommended for Northwest Africa.</p>