The quantitative and qualitative degradation of groundwater resources has become a serious crisis due to high consumption in agriculture, population growth and urbanization, and the industrialization of communities. Rehabilitating groundwater aquifers is one of the main requirements in aquifer management. In this study, the effect of improving the performance of irrigation district and, of course, reducing waste in the process of transfer, distribution and delivery of agricultural water, balancing and rehabilitating aquifers were examined. For this purpose, in the first step, the numerical model of Qazvin aquifer, with the code MODFLOW, was developed for spatial equilibrium analysis of aquifer. Then, the hydraulic simulator model of agricultural water distribution system flow in MATLAB software was developed, calibrated and verified and the automatic control system of the distribution system was linked with the automatic control model. Finally, by linking the developed models, the effect of using the method of improving the operation of the irrigation district, in the form of a scenario for balancing the aquifer, was examined. The results showed that with the improvement of the performance of the agricultural water distribution system, even in low water conditions, the average efficiency index of agricultural water distribution in agricultural areas in the decentralized automatic control system has been about 32. 7%. Accordingly, the rate of decline in aquifer harvest was 45. 3% in the decentralized automatic operation method. The results of numerical modeling of aquifer for spatial analysis of aquifer balancing showed that in the usual method of groundwater level operation, the increasing trend continues to decrease. The results show an annual drop of about 150 cm under the usual method of operation. By using a decentralized automatic control system and increasing the adequacy of water delivery in this method, this increased the level in the observation wells located in the irrigation district. The equilibrium solution for aquifers presented in this study can be developed for all agricultural areas (irrigation district) whose water supply sources are a combination of surface and groundwater resources.