Bacterioplankton and bacterioperiphyton composition was analyzed using the CARD-FISH technique in three shallow lakes of the Pampean Plain (Argentina) with contrasting regimes: clear vegetated, turbid due to phytoplankton and turbid inorganic, due to inorganic particles. We postulated that these differences would influence the proportion of the main bacterial groups both in periphyton and in plankton. The turbid lake due to phytoplankton presented the highest total abundances in both communities. Alphaproteobacteria was the dominant group in the three lakes in both communities. Redundancy analysis (RDA) evidenced that the bacterioplankton structure was different among lakes and mainly influenced by dissolved inorganic nitrogen and conductivity. On the other hand, for the bacterioperiphyton, RDA showed that bacterial group abundances increased with higher periphytic chlorophyll-a values. In the clear lake the relative abundance of Betaproteobacteria and Cytophaga increased in the bacterioperiphyton towards the end of the colonization. Our study suggests that the lake regime (clear or turbid) influence the structure of bacterioplankton and bacterioperiphyton.