At present, there are two sets of groundwater monitoring data in China, which are manual submission (manual stations) data and automatic transmission (automatic stations) data. Groundwater monitoring data plays an important role in revealing the dynamic distribution characteristics of groundwater and providing statistical support for the control of its overexploitation. Therefore, it is necessary to evaluate and compare the quality of the groundwater depth data measured by different monitoring systems. Based on the measured data of groundwater depth from 2 800 manual stations and 1 0298 automatic stations in the same period of 2018, we adopted statistical methods to evaluate the quality of groundwater monitoring system data from four aspects of integrity, rationality, representativeness and consistency. The results show that the average missing rate of groundwater depth data of automatic stations was reduced from 13.53% to 6.39%, and the abnormal rate was reduced from 1.63% to 0.84% compared with that of the manual stations. The difference of spatial distribution characteristics of the two sets of data, and its comparability of dynamic change trends all indicate that the quality of groundwater depth data of the National Groundwater Monitoring Project is better than that of the original manual stations.