<p>Despite the key role of bacteriobenthos in the biogeochemistry of coastal wetlands, the drivers controlling their diversity, distribution, and assembly at the freshwater-seawater transition remain unclear, particularly in tropical regions. Based on 16S rRNA gene amplicon sequences, we analyzed how benthic bacterial communities in floodplain lakes change along a salinity gradient in the Grijalva-Usumacinta deltaic plain (GUd) in southeast Mexico. Diversity was significantly higher in the low salinity portion of the delta and decreased towards higher salinities. However, lower diversity was also observed in a freshwater lake with the highest water chlorophyll <i>a</i> concentration, presumably indicating the detrimental role of eutrophication on diversity. Most bacterial sequences were assigned to Proteobacteria, Acidobacteria, Bacteroidetes, Chloroflexi, and Firmicutes. Among Proteobacteria, Gammaproteobacteria (including former Betaproteobacteria) dominated in low salinity and Alphaproteobacteria in higher salinity. The most abundant members of these groups participate in the biogeochemical cycles of major elements. Others are commonly associated with sewage, heavy metals, and hydrocarbons. Our results support the hypothesis that there are spatial changes in the bacteriobenthos structure of GUd floodplain lakes, reflecting changes in site conditions along the salinity gradient. As in other coastal regions, salinity featured as the main driver of bacterial diversity and composition, although nutrient availability also played an important structuring role. As coastal wetlands face multiple human stressors, such as saltwater intrusion, unsustainable use, and pollution that may cascade into significant ecosystem changes, research on bacterial communities is essential for gaining a deeper understanding of the complex dynamics of these wetlands.</p>