Abstract: Due to the shortage of fresh water, groundwater is the main resource for irrigation in arid oasia. In the present study, the impacts of ten-year irrigation with brackish ground water on soil microbial biomass and enzyme activity were compared to those of fresh water in a cotton farming system. The results showed that total salt content changes were significantly greater in soil receiving long-term saline groundwater irrigation (P<0.05), compared with fresh water irrigation, total soil salt content and exchangeable sodium percentage(ESP) increased by 61.5% and 3.2 times, respectively. In the salt affected soil, total enzyme activities of cellulose, urease, invertase and catalase decreased by 21.3%, 50.9%, 50% and 10.5%, respectively. By contrast, soil alkaline phosphatase and polyphenol oxidase activities increased significantly (P<0.05) with increasing salinity and sodicity. Long time brackish groundwater irrigation caused deleterious effects on soil microbial biomass, with biomass carbon and biomass nitrogen decreasing by 24.4% and 42.4%, respectively. However, no obvious detrimental effect of salinity on soil microbial biomass phosphorus was observed. Microbial biomass and enzyme activities were closely related to soil fertility in cotton fields. Organic matter and total nitrogen with the long-term brackish ground water irrigation decreased by 26.8% and 28.0%, respectively. These results reveal that long-term saline groundwater irrigation not only influences the chemical and physical characteristics of soils, but also directly affects soil biological properties and, therefore, has important implications for soils health and sustainability in arid agricultural areas.