Investigating the characteristics and influencing factors of groundwater drought, and identifying their difference in the regions with different climate conditions can provide an essential reference for the sustainable management of groundwater resources. As a case study in the two largest and typical catchments in China, the temporal evolution, spatial distribution and trend characteristics of groundwater drought are identified by GRACE-based groundwater drought index in the Yangtze River catchments (YZRC) with a humid climate condition, and Yellow River catchments (YRC) with an arid/semi-arid climate condition. Their influencing factors, which include natural net recharge (P-ET), teleconnection factors (ENSO, PDO and AO), and anthropogenic factors (land use and land cover, LULC), are investigated and quantitatively compared based on Pearson correlation analysis, cross wavelet transform and Random Forest. The results indicate that: (1) The groundwater droughts in the YZRC mainly occur during 2002–2009, which are mostly in the middle and lower reaches of the catchments, and they show a decreasing trend in most regions of the catchments. In the YRC, they mainly occur during 2015–2019, which influence almost the whole catchments, and they show an increasing trend in most regions of the catchments. (2) The P-ET has a significant positive impact on the mitigation of groundwater drought in the YZRC, while it fails to reverse the groundwater drought aggravation in the YRC. The teleconnection factors have obvious influences on groundwater drought evolution, among which Arctic Oscillation (AO) and Pacific Decadal Oscillation (PDO) are the important factors affecting groundwater drought in the YZRC and YRC, respectively. For LULC, the decrease of cropland and grassland could alleviate groundwater drought in the YZRC, and the increase of grassland, forest and urban area in the YRC could aggravate groundwater drought in the catchments. (3) When quantitatively comparing the contributions, the LULC and P-ET are the crucial factors affecting groundwater drought in the two catchments, while in the YRC, the impact of teleconnection factors cannot be ignored, although it is relatively weak. Moreover, groundwater exploitation plays an important role on groundwater drought in the YZRC and YRC. Its contribution in the YZRC and YRC is slightly lower than that of P-ET, but obviously higher than that of teleconnection factors.

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