Aquatic ecosystems are critical components of the global environment. One of the most important issues that has not been elucidated in aquatic ecology concerns the long-term effect of climate change on the ecosystem stability. Due to the role it plays in aquatic ecosystems, understanding how microbial communities respond to climate change is a major challenge. Our investigations focused on the microbial diversity in water and sediments from Danube Delta, in relation with the spatial distribution and geochemistry. The samples for this study were collected from 11 sites that cover all the important regions of the Danube Delta. The physico-chemical analysis performed for each site indicates the presence of reduced quantities of organochlorinated compounds in most of the analyzed samples. A high content of γ-HCH (Lindan insecticide), respectively the isomer β-HCH and PCB were measured in Caraorman and Crișan sampling points. Illumina MiSeq sequencing of 16S rRNA gene carried out on water and sediment samples highlighted variations of bacterial diversity with the type of habitat, location and geochemical characteristics. The microbial community consists of several bacterial phylum, of which Firmicutes, Proteobacteria, Actinobacteria and Bacterioidetes are the most abundant. No seasonal variability was detected, the main community members in all samples being affiliated with the Firmicutes and Proteobacteria strains. However, in the cold season (October) it was observed an increase in the relative abundance of Firmicutes, from > 50% to > 60%. Patescibacteria (4.6%) and Tenericutes (25.8%) are present in relatively high abundance in one of the sampling points, being followed by Bacteroidetes and Proteobacteria with a higher relative abundance in other sites. Associations between microbial diversity and pesticide content indicate the possibility of a link between community structure and the presence of organochlorine pesticides.