A model simulating the transport of water and nitrate in soil under mulched drip irrigation of cotton was established and solved numerically by using the HYDRUS-2D package. The model was calibrated and validated by the field experiments conducted in Urumqi, Xinjiang Uygur Autonomous Region, China, during the cotton growing seasons of 2010 and 2011. The emitter discharge rates that progressively decreased from the inlet to the distal end along the dripline were discretized as a series of sequential segments each having an equal discharge rate. Assuming no lateral exchange of water in soil between adjacent segments, the model, which had been verified, was used to evaluate the effect of drip system uniformity and soil spatial variability on the distributions of water and nitrate in soil under arid conditions. The results indicated that the uniformity coefficients of soil water content and nitrate were observed in downward trend for drip system uniformity coefficients (Cu) of 0.60 and 0.80, while a relatively stable variation pattern was observed for Cu=0.95; the lower system uniformity the greater decrease in the uniformity coefficient of soil water content and nitrate following an irrigation event was observed. The uniformity coefficient of soil nitrate, which varied from 0.35 to 1.00, was substantially lower than that of soil water content. Meanwhile, the soil spatial variability in the experimental field increased the nonuniform distributions of the soil water and nitrate.