Population growth combined with intensified agro-industrial activity in the Greater Casablanca region has increased pollutant inputs into adjacent aquatic systems, requiring robust ecological assessment tools. This study evaluates, for the first time, the ecological quality of five wadis in this region using benthic diatoms as bioindicators integrated with physicochemical parameters and an organic pollution index. Eleven stations distributed along an upstream–downstream gradient (Nfifikh, El Maleh, Hassar, Bouskoura, and Merzeg wadis) were surveyed during wet and dry seasons of 2024. Ecological status was assessed using the Generic Diatom Index (IDG), Specific Polluosensitivity Index (IPS), and Diatom Saprobic and Eutrophication Index (IDSE), and compared with the Organic Pollution Index (IPO). Community structure was analyzed through taxonomic composition and multivariate analysis. Numerical results show strong spatial differentiation of ecological conditions. One station (EM1) exhibits oligo-mesotrophic conditions with good to moderate ecological status (IDG up to 13.01; IPS up to 13.12; IDSE up to 3.6), whereas B1 reflects intermediate degradation with mesotrophic to eutrophic conditions (IDG 9.02–10.17; IPS 8.45–9.17). The remaining stations (N2, EM2, H1–H2, B2, M1–M2) consistently fall into poor to very poor ecological classes, with hypereutrophic conditions and dominant pollution-tolerant taxa, particularly Nitzschia spp. Correlations between diatom indices and IPO are highly significant (p < 0.01). Notably, 14 taxa are newly reported for Moroccan freshwater ecosystems. The study is limited by incomplete seasonal accessibility of certain stations, which may reduce temporal resolution of community dynamics. Nevertheless, the results provide a coherent ecological diagnosis across heterogeneous hydrosystems. Practically, the findings support the use of diatom-based indices as integrative tools for monitoring cumulative pollution impacts and distinguishing eutrophication from organic loading. The originality of the study lies in the first basin-wide diatom assessment of Greater Casablanca wadis combined with multi-index comparison and first records of regional taxa. This establishes a baseline for future ecological monitoring and comparative studies in North African semi-arid river systems.