Existing studies on water resource issues focus on water scarcity while largely lacking an integrative water balance health assessment and ignoring the combined impacts of water quality, water transfer, and unconventional water resources on water balance. Here, we proposed a novel framework for assessing regional water balance health considering three dimensions of water problems about imbalances: water scarcity, water inequality, and systems incoordination. This paper first quantified the levels of water balance health at multiple geographic and temporal scales in China, and then investigated the critical components and the impacts of improved surface water quality, inter-basin water transfer, and unconventional water use on the local water balance health. Results showed that China was under an unhealthy water balance due to multiple imbalances based on the annual average assessments during 2014–2018. More than 45% of the national population (∼615 million people) was affected by an unhealthy water balance. Hotspots with unhealthy water balance exhibited spatial heterogeneity and temporal variability, with Northern China experiencing unhealthy water balance throughout the year, while Southern China usually faced this issue during the winter. Unhealthy water balance in Northern China was primarily driven by water scarcity, while in the west of the Hu-Huanyong Line, water inequality exacerbated the situation. Southeastern China faced systems incoordination, particularly vulnerable during extreme events, such as severe droughts. More than 400 and 150 million people benefited significantly from improved surface water quality and inter-basin water transfer, respectively, relieving unhealthy water balance. However, the effectiveness of unconventional water use was found to be limited. This study contributed to a better understanding of water balance health and facilitated the development of policies for integrated water resources management in China.