Man-made reservoirs which receive substantial inputs of terrestrial organic matter are characterized by physiologically diverse and distinct bacterial communities. Here we examined bacterial community structure using Illumina MiSeq sequencing of 16S rRNA genes and evaluated the potential role of viruses in influencing them in two productive freshwater reservoirs namely, Villerest and Grangent (Central France). Two dimensional nonmetric multidimensional scaling analyses indicated that bacterial communities in both reservoirs were structurally different in time and space, with Villerest harboring more diverse communities than Grangent reservoir. The bacterial communities in both reservoirs were dominated by hgcI clade (Actinobacteria) and Limnohabitans (Betaproteobacteria) which are known to have adaptive life strategies towards top-down mechanisms and resource utilization. In Villerest, thermal stratification of water column which resulted in temporary anoxia especially during summer promoted the occurrence of anoxygenic phototrophic and methanotrophic bacteria. Overall, low bacterial richness which was linked to viral lytic infection possibly suggests that a relatively small number of highly active bacterial populations sustained high bacterial activity and viral abundances. Weighted UniFrac analysis indicated that a minimum threshold viral infection and virus-to-bacteria ratio (serve as a proxy) of 10% and 10, respectively, is required to exert its impact on phylogenetic structure of bacterial community. Therefore depending on the levels of viral infection we suggest that viruses at times can prevail over other trophic or top-down factors in shaping and structuring bacterial communities in such man-made artificial freshwater systems.