The water use struggle among different sectors is a serious water resource problem during the drought in Taiwan. The irrigational use water is frequently been transferred to industrial use water due to its lower economic value, although agriculture sector will be compensated from other water use sectors when water transfers occur, the reasonable amount of compensation is still controversial How to obtain a quantitative support for helping different water use sectors to achieve an acceptable resolution is vital. Therefore, this study develops a multiobjective model of water resource management to evaluate the trade-off among different water use sectors. The shortage index is used to perform the water deficit of different water use sectors. The model integrates operating rules, stepwise linear programming (SLP) and multiobjective genetic algorithm (MOGA) to solve a mutiobjective regional water allocation problem. Moreover, simulation results clearly demonstrate the trade-off relationship between shortage indexes for agriculture and that for industry. The computed trade-off curve, non-inferior solutions, is a valuable quantitative support for the transfer negotiation of water use among various sectors.