The presence of brackish water resources is significant in addressing the scarcity of freshwater resources, particularly in the Xinjiang region. Studies focused on reducing adverse effect of brackish water irrigation based on using ionized brackish water, as well as on investigating its effects on fibre and oil plant production processes, remain incipient in the literature. Some benefits of this technique are the optimization of the quality and quantity of irrigation water, economy of water absorbed by the plants, improvement in the vegetative growth and productivity compared to irrigation using conventional brackish water. Thus, the aim of the current study is to assess the effect of different nitrogen application rates on soil water and salinity, cotton growth and water and nitrogen use efficiency. The experimental design consisted of completely randomized design with two water types (ionized and non-ionized) and six nitrogen application rates with four replications. Irrigation conducted with ionized brackish water and different nitrogen application rates had significant effect on the plant height, leaf area index, shoot dry matter, boll number per plant and chlorophyll content. The study also demonstrated significant effects of ionized brackish water on soil water content and soil salinity accumulation. The highest cotton production was achieved with the use of 350 kg·ha-1 of ionized brackish water for irrigation, resulting in an average increase of 11.5% compared to the use of non-ionized brackish water. The nitrogen application exhibits a quadratic relationship with nitrogen agronomic use efficiency and apparent nitrogen use efficiency, while it shows a liner relationship with nitrogen physiological use efficiency and nitrogen partial productivity. After taking into account soil salinity, cotton yield, water and nitrogen use efficiency, the optimal nitrogen application rate for ionized brackish water was determined to be 300 kg·ha-1. It is hoped that this study can contribute to improving water management, reducing the environmental impact without implying great costs for the producer.