To evaluate the impacts of the Middle Route of the South-to-North Water Diversion Project on groundwater depth in the water-receiving areas of Henan Province, this study systematically investigated the spatiotemporal evolution of groundwater depth and its influencing factors before and after project operation, based on monitoring data from 2004 to 2024, using geostatistical methods and principal component analysis. The results indicate that following project operation, the ratio of groundwater supply to allowable groundwater withdrawal decreased from 216.50% to 175.09%, representing a reduction of 41.41 percentage points and indicating an alleviation of groundwater overexploitation pressure. After project operation, the areal proportion of the 0–8 m groundwater depth interval decreased by 14 percentage points relative to the pre-operation period, that of the 8–28 m interval increased by 14.2 percentage points, and that of the >28 m interval decreased slightly. After project operation, the spatial variability of groundwater depth changed, and the nugget-to-sill ratio exhibited fluctuating behavior: it decreased during 2015–2021, indicating a stage-wise strengthening of spatial dependence; in 2022, the nugget-to-sill ratio increased sharply and spatial autocorrelation weakened; and overall, the ratio fluctuated within the strong to moderate spatial autocorrelation range. The PLSR-VIP analysis identified surface water supply and domestic water consumption as the two highest-ranked factors associated with groundwater depth. Although diverted water volume had a full-sample VIP of 1.010, its VIP exceeded 1 in only 38.1% of leave-one-year-out refits and decreased to 0.825 after detrending, with a non-significant detrended correlation (r = −0.228, q = 0.356). These findings indicate that its statistical importance was sensitive to sample composition and temporal trends. During 2015–2024, groundwater depth exhibited a decreasing trend, indicating groundwater-level recovery, coinciding with changes in the regional water supply structure. However, the independent contribution of the diversion project to this recovery could not be established from the present analyses.