Because the relevant environmental damages were not incorporated into evaluating conventional water-use efficiency, this efficiency indicator was incapable of depicting the real comprehensive effects except economic outputs. The concept of environment-economy integrated efficiency for regional water use(WEEE) was raised along with its evaluation method based on a combination of DEA and Malmquist index. The WEEE of Henan province was then studied by using the data on water uses and related economic outputs and pollution discharges from 2001 to 2012. In contrast to a higher level economic efficiency, a lower level environmental efficiency had been witnessed for water uses of the province. To a large extent due to a poor environmental efficiency, the provincial WEEE was dragged down by about 2% if compared to the sole economic efficiency. Meanwhile, the cities with WEEEs of inefficient DEA in the province had exhibited the problems of low efficient water uses and excessive pollutant discharges. The averaged input redundancy rate of water resource reached 18% in 2012, and the extra emission rates of COD and NH₃-N were about 49% and 49.2% respectively. An analysis of variations of the total factor productivity(TFP) indicated that the technical change index was the most influential factor, resulting in an annually averaged decline of 2% in Henan's WEEE in the study period. Thus, it was recommended that more inputs need be made into technical innovations to realize water saving and water pollution control. The total volume control of water use should be enforced along with abatement of water pollutants.