<p>New strategies for irrigating tomato crops using brackish water (BW) combined with biogas slurry (BS) were assessed over two growth seasons in western arid regions of China. BW at three levels of salinity (2, 3, and 5&#xa0;g/L) combined at a ratio of 1:4 with BS was applied to tomato plants at three growth stages (seedling, flowering/fruiting, and maturity) to identify the optimal model for integrated irrigation. The experiment comprised nine treatments, each applied during the 2022 and 2023 seasons. Overall, irrigation with BW-BS increased soil moisture, total nitrogen, and pH in the tomato root zone. Specifically, plant growth responded positively to receiving BW-BS in a low-moderate-high salinity sequence over the three growth stages (T4), which promoted plant height, stem diameter, and dry matter accumulation. Moreover, T4 increased Na⁺, Ca²⁺, and Mg²⁺ accumulation in the soil, elevated Na⁺ levels in roots, and facilitated the distribution of Ca²⁺ to aerial parts. Fruit quality characteristics under T4 excelled in terms of fruit shape index, hardness, soluble sugars, sugar-acid ratio and vitamin C content. The salinity sequence under T3 (high-moderate-low), enhanced the accumulation of Mg²⁺ in fruit and outperformed T4 for fruit water content, titratable acidity, soluble solids, and proteins. However, T7, which provided unchanging low levels of saline over the three growth stages, resulted in the highest comprehensive evaluation score of tomato quality. Yield and irrigation water use efficiency (IWUE) decreased under all treatments compared to the freshwater control, but T4 showed the least decline in yield and IWUE, and the highest score in the comprehensive benefit evaluation, suggesting that staged salinity management can mitigate the negative effects of BW. This approach expanded the potential of utilizing marginal water resources and provided a sustainable solution for managing BS and water resources for agriculture in arid regions like Northwest China.</p>