This study investigates biodiversity and structure of spring diatoms associations from Sebou Basin, one of Morocco's largest superficial hydrosystems. The physico-chemical results reflect both anthropogenic and natural pollution, mainly from mineral sources. 226 taxa were identified, 92% are pennates. The result of Shannon and equitability indices showed that diatom populations were generally diversified, which depends on degree of specific richness at each station. Thus, the higher number of taxa in site Og (120 species) reflects an ecologically more stable and more diversified ecosystem dominated by E. minuta, opposed to S1 (Sebou) and B2 (Beht), which have an unbalanced community represented by smaller numbers of taxa (48 in S1 and 52 in B2) strongly dominated by N. capitellata and N. palea. The Canonical correspondence analysis distinguished three groups: group 1 with S0, B1, Og and In located far from pollution sources, group 2 composed of polluted sites (S1 and B2), while group 3 with of S2, S3, and S6 are located in the lower section of the Sebou Basin. Multi-response permutation procedures confirmed the three site groupings. It was found that the water quality located downstream from the urban rejections is degraded, indicator species analyses showed a succession of changes in diatom species from upstream sites to downstream. Six species were determined as indicator species; Groups 1 and 2 only had one species each, G. olivaceoides (86%) and H. amphioxys (87%), respectively, while group 3 had four species, N. recta (93%), N. sigma (95%), N. tripunctata (96%) and D. oblongella (100%).