Accomplishing the objectives of optimal and sustainable management in the agricultural sector is increasingly getting complicated, which includes increasing the sustainable productivity of water and energy resources, ensuring food security, decreasing contaminations from fertilizers and chemical pesticides, and environmental destruction. The present research deals with designing the relationships between the water-energy-food (WEF) nexus approach with economic and environmental objectives to accomplish the aforementioned objectives. Hence, a multi-objective programming model was developed to maximize the water-energy-food nexus index and farmers' gross margin, minimize the use of chemical fertilizers (nitrogen and phosphate), and minimize the use of chemical pesticides (herbicides) by considering the balancing constraint to groundwater resources. Afterward, the proposed multi-objective model was solved using the augmented ε-constraint method, and then the total of strong and efficient Pareto solutions was extracted. Then, the best solution was chosen using the TOPSIS method and assigning a weight of equal importance to the desired objectives. The irrigation network of Jiroft plain in Kerman province in Iran was chosen as the study area to implement such a system. The obtained results indicated that the optimal and sustainable management in the agriculture sector can be hopeful using the proposed approach in the current research. On the other hand, the results revealed that despite considering the economic objective in the proposed system, the farmers' profits can be significantly decreased. Thus, the realization of optimal and sustainable management in the agricultural sector is not possible without the implementation of policies for increasing the economic incentive of farmers.