Water environmental capacity (WEC) is an essential indicator for effective environmental management. The designed low water flow condition is a prerequisite to determine WEC and is often based on the stationarity assumption of low water flow series. As the low water flow series has been remarkably disturbed by climate change as well as reservoirs operation and water acquisition, the stationarity assumption might bring risk for WEC planning. As the reservoir operation and water acquisition under climate change can be simulated by a water resources allocation model, the low water flow series outputted from the model are the simulations of the disturbances and often show nonstationary conditions. After estimating the designed low water flow through nonstationary frequency analysis from these low water flow series, the WEC under the nonstationary conditions can be determined. Thus, the impacts of water resources allocation on WEC under climate change can be quantitatively assessed. The mid-lower reaches of the Hanjiang River basin in China were taken as a case study due to the intensive reservoir operation and water acquisition under the climate change. A representative concentration pathway scenario (RCP4.5) was employed to project future climate, and a Soil and Water Assessment Tool (SWAT) model was employed to simulate water availability for driving the Interactive River-Aquifer Simulation (IRAS) model for allocating water. Water demand in 2016 and 2030 were selected as baseline and future planning years, respectively. The results show that water resources allocation can increase the amount of WEC due to amplifying the designed low water flow through reservoir operation. Larger regulating capacities of water projects can result in fewer differences of WEC under varied water availability and water demand conditions. The increasing local water demand will decrease WEC, with less regulating capacity of the water projects. Even the total available water resources will increase over the study area under RCP4.5. More water deficit will be found due to the uneven temporal-spatial distribution as well as the increasing water demand in the future, and low water flow will decrease, which further leads to cut down WEC. Therefore, the proposed method for determining the WEC can quantify the risk of the impacts of water supply and climate change on WEC to help water environmental management.