Bacterioplankton is an essential component for the functioning of aquatic ecosystems and has a profound impact on the water quality of the aquatic environments. It is therefore important to increase knowledge about its dynamics and genetic diversity. The main objectives of this work were to evaluate the structure and dynamics of bacterioplankton from four Pampean shallow lakes located in the upper (Gómez and Carpincho) and lower (Chascomús and El Triunfo) basins of the Salado River, as well as to determine the influence of environmental factors on these communities. To achieve this, seasonal samplings were performed during one year (January 2015-January 2016), in which main limnological variables were determined and the structure of bacterioplankton was analyzed by means of Illumina next-generation amplicon sequencing of the 16S rRNA gene. Bacterioplankton diversity indices were significantly higher in shallow lakes from the upper basin relative to those of the lower basin. Bacterioplankton richness was significantly lower in the clear-regime and disconnected shallow lake (El Triunfo) than in the turbid-regime and connected shallow lakes (Gómez, Carpincho and Chascomús). Bacterioplankton composition differed between all shallow lakes, except between the nearby and interconnected shallow lakes (Gómez and Carpincho). Environmental variables, such as total phosphorus, conductivity and Secchi depth, influenced the bacterioplankton composition in the studied lakes. Similarity in the bacterioplankton composition increased significantly with higher environmental similarity between lakes and decreased with spatial distance between them. Our results showed the bacterioplankton structure of the studied lakes was ruled by environmental and spatial factors. The bacterial structure varied between basins, and also between systems with different regimes and/or connections to the river.