In shrimp aquaculture, shrimp farming systems are carefully determined to avoid rearing failure due to stress, disease or mass mortality, and to achieve optimum shrimp production. Little is known about how shrimp farming systems affect environmental parameters and bacterial community in rearing water, whether high stocking densities (intensive system) will increase the abundance of pathogenic bacteria. Moreover, high content of suspended particulate matter in shrimp pond potentially load more bacteria, including pathogenic bacteria, which then can be used as a sentinel of the potential presence of pathogenic bacteria in shrimp farming. Therefore, water parameters and the abundances of cultivable heterotrophic bacteria, including potential pathogenic Vibrio, were measured in three ponds of moderate/semi-intensive (40 post-larvae m-3) and three of high density/intensive shrimp aquaculture (90 post-larvae m-3), at day 10, 20, 30, 40, 50, and 70 of rearing. Additionally, free-living and particle-attached bacterial communities in the pond water were analyzed via 16S amplicon sequencing. Among the observed environmental parameters, suspended particulate matters, salinity, chlorophyll a, pH and dissolved oxygen differed significantly between the intensive and semi-intensive systems. However, no significant difference was observed for inorganic nutrients, abundances of heterotrophic bacteria, and potential pathogenic Vibrio between two systems. Bacterial communities were dominated by Gammaproteobacteria, Alphaproteobacteria, Flavobacteria, Bacilli, and Actinobacteria. Operational taxonomic units (OTUs) of the genera Halomonas, Psychrobacter, and Salegentibacter were present in both systems, where they may be involved in nitrification and ammonium removal. Halomonas, Psychrobacter, and Vibrio were most abundant genera in the particle-attached fractions, while Salegentibacter, Sulfitobacter, and Halomonas were found in the free-living fractions of both systems. Furthermore, aggregates of intensive systems loaded more Vibrio than semi-intensive ones. Interestingly, when the sequence proportion of Halomonas or Psychrobacter decreased, the proportion of Vibrio increased. Redundancy analysis showed that among the observed environmental parameters, salinity was best suited to explain patterns in the composition of both free-living and particle-attached bacterial communities (R²: 15.32% and 12.81%, respectively). In conclusion, intensive systems affected water quality and increased prevalence of potentially pathogenic bacteria, although they did not seem to promote a more diverse bacterial community.