Data and knowledge of the spatial-temporal dynamics of surface water area (SWA) and terrestrial water storage (TWS) in China are critical for sustainable management of water resources but remain very limited. Here we report annual maps of surface water bodies in China during 1989-2016 at 30m spatial resolution. We find that SWA decreases in water-poor northern China but increases in water-rich southern China during 1989-2016. Our results also reveal the spatial-temporal divergence and consistency between TWS and SWA during 2002-2016. In North China, extensive and continued losses of TWS, together with small to moderate changes of SWA, indicate long-term water stress in the region. Approximately 569 million people live in those areas with deceasing SWA or TWS trends in 2015. Our data set and the findings from this study could be used to support the government and the public to address increasing challenges of water resources and security in China.