Water shortage, which can greatly affect both natural systems and social development, has drawn extensive attention from governing authorities around the world, and become an urgent issue to be addressed. How to improve the green efficiency of water resources and alleviate the present situation of water shortage is the content of this study. In the concept of "people-oriented" green development, the evaluation system of green efficiency is constructed, which includes four aspects: nature, social economy, environment, science and technology. This paper, based on the panel data of 31 provincial-level regions of China obtained from 2000 to 2016, aims to calculate the green efficiency of water resources by applying the Super-efficiency SBM model, to analyze its spatial correlation pattern, and to explore the driving mechanism of green efficiency of water resources by making use of the geographical weighted regression (GWR) model. The results show that there was ignificant positive spatial correlation and uneven spatial distribution of the green efficiency of water resources in China. Compared with the OLS model (the regression coefficient obtained by the model just represents the average characteristics of the overall green efficiency of water resources), the GWR model proves that there were spatial differences in the influence of various factors on the green efficiency of water resources. Generally speaking, industrial structure, industrial and agricultural development level, transportation infrastructure construction, environmental protection investment and science and technology conversion rate had a positive effect on the green efficiency of water resources, while the factors, including per capita water resources, population size and pollutant emissions, had a restraining influence. Social factors and environmental factors had a particularly obvious effect on the green efficiency of water resources. In addition, due to the large potential of the technology market turnover, the regions should step up efforts to increase investment of scientific research and focus on the transformation of scientific research results so as to make technology a new growth pole of green efficiency of water resources. In terms of spatial differences, water endowment and population size had significant impact on the green efficiency of water resources in the western region, and industrial structure, water utilization structure and transportation infrastructure posed a positive effect in the eastern region. This study is of great practical significance to solve water shortage and to formulate relevant policies suitable for the development of all regions.