Abstract: In the programming of water pollution control system the combined method of optimization with simulation is used generally,it is not only laborious in calculation,but also the global optimum of the obtained solution is difficulty guaranteed.In this paper,the genetic algorithm （GA） used in the nonlinear programming of water pollution control system is given,by which the preferred conception for the programming of wasted water system is found in once-through operation,it is more succinct than the conventional method and the global optimum of the obtained solution could be ensured.