Irrigation with saline water alters the soil environment, thereby influencing soil microbial processes and crop growth. The objective of this field experiment was to compare the effects of long-term irrigation with saline water or freshwater on cotton growth, soil physicochemical properties, and bacterial community structure. High-throughput sequencing of DNA of the 16S rRNA gene was used to assess the composition of bacterial communities. Saline-water irrigation significantly increased soil salinity and significantly decreased pH, soil organic matter, total nitrogen, and biomass and yield of cotton. Cotton biomass and yield were negatively correlated with soil salinity but were positively correlated with soil organic matter, and total nitrogen. Compared with fresh water irrigation, irrigation with saline water significantly decreased the Shannon diversity index of the bacterial community. Compared with freshwater irrigation, saline-water irrigation significantly increased the relative abundance of two phyla of bacteria (Gemmatimonadetes and Actinobacteria) and decreased that of two (Proteobacteria and Acidobacteria). In addition, the relative abundance of 5 genera was significantly higher (Sphingomonas, Gemmatimonas, Gaiella, Solirubrobacter, and Nocardioides) and that of 7 was significantly lower (RB41, H16, Haliangium, Nitrospira, Lysobacter, Acidobacteria_bacterium, and Bryobacter) in the saline-water treatment. Soil salinity and pH were the major environmental factors that shaped bacterial communities. According to LEfSe analysis, only 3 indicator species were associated with saline-water irrigation, whereas 5 indicator species were associated with freshwater irrigation. Overall, long-term irrigation with saline water adversely affected soil properties and led to decreases in soil bacterial community diversity and cotton growth and yield. These results contribute to a more comprehensive understanding of bacterial communities in saline environments.