Determine which processes take place in the spatial distribution of bacterioplankton metacommunities has been a central goal of microbial ecology. In freshwater systems, selection has been spotted as the main driver shaping bacterial community structure. However, its relative importance compared with others processes (i.e. dispersal, drift, speciation) may depend on spatial heterogeneity and dispersal rates within a metacommunity. Here, we investigate the main ecological processes modulating the bacterial assembly in contrasting scenarios of environmental heterogeneity. We carried out a spatiotemporal survey in the complex floodplain system of Paraná River and predicted that, as the system becomes more homogeneous, the bacterioplankton metacommunity would be mainly driven by non-selective processes leading to more random associations between bacteria taxa. Contrarily, we found that selection was the main process even at both environmental heterogeneity and homogeneity, challenging the general view that the strength of the selection is weakened due to dispersal homogenization. Still, the relative importance as well as the type of selection, changed with environmental heterogeneity. At high and low environmental heterogeneity, heterogeneous and homogeneous selection had the major role in structuring the metacommunity, respectively. At intermediate environmental heterogeneity, the relative importance of non-selection processes was twice as high compared with the other phases and the selection acted with similar strength both homogenizing and segregating the communities. The ecological processes acting on the bacterial community also determined the complexity and randomness of bacterial networks. The heterogeneous selection promoted greater network complexity increasing the niche habitat heterogeneity and the taxonomic β-diversity. Additionally, the bacterial associations were more random when stochastic processes had more influence over bacterial communities. Finally, the spatiotemporal heterogeneity was an important factor determining the keystone in the system. Integrating all these empirical evidences we devised a new conceptual model that states how the environmental heterogeneity guild the action of ecological processes that modulate the metacommunity bacterial assemblage.