To alleviate surface water shortages during cotton (Gossypium hirsutum L.) cultivation in Xinjiang, the largest cotton producing area in China, we used brackish groundwater resources for mulched drip irrigation in a field. Soil moisture, salinity accumulation, pH, ion concentrations, water-use efficiency, and cotton yield were compared when irrigated using brackish water with five salinities (1g·L−1; 3g·L−1; 6g·L−1; 9g·L−1; and 12g·L−1). Salinity accumulation was significantly stronger in the top soil (0–20 cm depth) than in the deeper soil layer (20–100 cm depth). The soil pH increased and cotton yield decreased accompanied as the brackish water salinity increased. After brackish water mulched drip irrigation was implemented during the cotton growth period, salinity accumulation and cotton yield showed significant differences among the brackish water irrigation treatments. When the salinity was less than 6g·L−1, the accumulated salt in the soil did not seriously affect water absorption by cotton, and the cotton yield was higher than when the salinity was more than 6g·L−1. Therefore, less than 6g·L−1 was a suitable salinity for cotton irrigation with brackish water. As the irrigation salinity increased, the cations gradually changed from Ca2+ to Mg2+ and K+, the anions gradually changed from SO42- and HCO3- to Cl−, and hydro-chemical facies gradually changed from SO42-·HCO3–Ca2+·K+ to SO42-·Cl–Ca2+·K+. This study provides guidance for the scientific management of the soil environment and the used of saline water irrigation for agriculture in the Xinjiang area of Northern China and other regions with similar environments.