The low water and fertiliser utilisation efficiency and soil quality degradation caused by high water and fertiliser inputs are the primary challenges facing goji berry cultivation in arid regions. A two-year field experiment was conducted from 2021 to 2022. The experiment included three irrigation rates (I1, I2, I3) of 2160, 2565, and 2970 m3hm-2 and three nitrogen application rates (N1, N2, N3) of 165, 225, and 285 kghm-2 to quantify their impacts on soil nutrients, enzyme activity, and goji berry yield in the root zone. Results indicate that the indicators of soil nutrients decrease with increasing soil depth, with depths of 0-20 cm accounting for 24.80-72.48% of total content. With fertility period progression, soil organic matter at depths of 0-80 cm exhibits a "folded-line" trend, while total nitrogen, nitrate nitrogen, and available phosphorus show an "M"-type trend. At depths of 0-40 cm, the proportions of urease, sucrase, and alkaline phosphatase activities all exceeded 70%. At I1 irrigation rate, enzyme activities gradually increased with rising nitrogen application rates. At I2 and I3 irrigation rates, enzyme activities first increased, then decreased with increasing nitrogen application. The highest yields of both fresh and dried fruits were achieved at I2N2 treatment, increasing by 14.17% and 14.78%, respectively, compared to conventional management (CK). Analysis of the random forest model indicates that the soil-driven factors influencing yield formation include SA, UA, APA, HPA, SOM, NH4+-N, and TP. Analysis of SQI and yield fitted data indicates that water-nitrogen coupling significantly influences wolfberry yield by regulating soil quality. Partial least squares (PLS-PM) showed that N application and irrigation of soil nutrients did not cause a significant indirect impact on goji berry yield, but a significant positive effect on goji berry yield occurred through enzyme activity.