In this study, littoral diatoms and environmental variables were sampled three times in 2017 (spring, summer, and autumn) to determine the effect of salinity (SAL) and altitude (ALT) on the littoral diatom assemblages (composition, distribution, species richness and diversity) of 12 lentic systems in the Western Mediterranean Basin. Due to the SAL and ALT differences in these systems, they were distinguished under two groups (high elevated freshwater lentic systems [HEF] and hyposaline lentic systems [HYP]). The Bray–Curtis and Canonical Correspondence (CCA) analyses based on diatom species also confirmed this separation. In HYP, SAL and alkalinity (ALK) were the most effective parameters on diatom assemblage. On the other hand, diatom assemblage was mainly affected by ALT in HEF. For the biological assessment of these systems, seven diatom indices were implemented. Although most of the indices showed higher regression with SAL and ALT, they did not give the intended result in the evaluation of HYP. On the other hand, the most consistent index with environmental variables and dominant species in HEF was the Generic Diatom Index (IDG).