Using both GRACE satellite data and statistical records, we apply the advanced Super-SBM model in this study to evaluate the efficiency of water resource utilization in 34 prefecture-level cities across three provinces in Northeast China from 2003 to 2020. Furthermore, we employ the Tobit model to examine the factors influencing efficiency. Our findings suggest that while spatial clustering is moderately low, the efficiency of water resource utilization in the Northeast Region is praiseworthy and significantly correlates with the level of technological advancement. Four distinct categories can be identified among the prefecture-level cities based on the scale and technological efficiency of water resource utilization. To promote enhanced utilization of water resources, different regions should implement measures that are specifically tailored to their unique circumstances.