To accurately obtain the spatial distribution characteristics of groundwater level in an extremely arid zone and its dynamic change patterns under the influence of human activities, based on the data of 55 groundwater observation wells in the middle and lower reaches of the Kriya River, spatial interpolation of regional groundwater level data were performed using the inverse distance weight, spline function, trend surface, and the ordinary kriging methods. The optimal interpolation method was selected by its accuracy to spatially interpolate the groundwater level data in the study area from 2019 to 2021. The results show that: (1) the ordinary kriging method has the highest interpolation accuracy (MAE = 7.1393, MRE = 0.0058, RMSE = 9.4314) and reflects the spatial and temporal variability and distribution characteristics of groundwater levels with great accuracy. (2)The relationship between surface water–groundwater recharge and discharge in different areas of the river channel in the desert section varies depending on geological structure, surface water seepage, and other elements. (3) Groundwater in the Taklamakan Desert has little effect on groundwater recharge in the Dariyabui Oasis, and changes in groundwater dynamics in the oasis are predominantly influenced by surface runoff. (4) Monthly changes in groundwater levels in the Yutian Oasis are continuous, with ‘V’ shaped fluctuations, a declining trend in the southern part, no significant change in the central part, and a slight increase in the northern part. These results contribute to the sustainable management of water resources in the Kriya River Basin, provide a basis for groundwater prediction, and offer a reference for studies of other, similar extreme desert area basins.