The microbial communities of aquatic ecosystems play crucial roles in maintaining environmental balance and ecosystem functions. This study aimed to compare the microbiomes of two Moroccan lakes, Aoua and Ouiouane, with those of three Moroccan rivers, the Oum Errabiaa, Moulouya, and Sebou Rivers. Using high-throughput sequencing of 16S rRNA gene amplicons, we analyzed the diversity and composition of the bacterial communities in these freshwater bodies. Our results revealed distinct lake and river microbial profiles, with significant differences in alpha and beta diversities. Lakes presented increased abundances of Cyanobacteria, Actinobacteria, Proteobacteria, and Bacteroidetes. In contrast, river microbiomes presented a greater prevalence of Firmicutes and Verrucomicrobia. The observed variations can be attributed to differences in environmental parameters such as nutrient availability, water physico-chemistry, and anthropogenic influences. These findings enhance our understanding of microbial biogeography in Moroccan freshwater systems.