By combining water right transaction with non-point source pollution control and considering the constraint conditions of planting area, agricultural water quota and pollutant concentration, a model for farmer's irrigation and fertilization behavior is employed by using the marginal analysis method, and the influences of the water right transaction and non-point pollution control on farmers' behavior are analyzed. The results show that the water consumption for irrigation is positively correlated to the price of crops and negatively related to that of transaction water and marginal irrigation cost. The application amount of fertilizer within a certain range is positively correlated to the price of crops, but it is negatively related to the marginal cost of fertilizer or marginal environmental cost. It is proved by the proposed model that the water market and water price policy will encourage the farmers to reduce water consumption for irrigation and to save water when the agricultural water quota can be transacted.