The escalation of crises related to water quantity of quality, energy, food, and the environment has posed numerous challenges to sustainable development in the agricultural sector. This study seeks to establish an optimal and sustainable framework within the agricultural sector by meeting the objectives of the WEF (Water-Energy-Food) nexus index and environmental. For this, we individually optimized the objectives: maximizing the WEFN index (O1), minimizing CO2 emissions (O2), reducing chemical fertilizer consumption (O3), minimizing chemical pesticide usage (O4), and maximizing gross margin (O5) under various electrical conductivity (EC) scenarios (optimistic, moderate, and pessimistic) within the irrigation network of the Jiroft plain in Iran. In the second stage, we employed a Multi-Objective Programming (MOP) Model to attain these objectives using a weighted sum approach simultaneously. The results of the first stage revealed that under moderate and pessimistic EC irrigation water scenarios, significant alterations in the crop selection within the optimized models for O1 and O5 objectives occurred compared to the baseline scenario, which did not consider EC irrigation water. Specifically, in the pessimistic scenario with an EC irrigation water level of 2.25 ds/m, crops such as onions, tomatoes, and potatoes were replaced within the optimal cropping pattern by wheat, barley, and green-maize, leading to a notable decline in program efficiency. The results from the MOP optimization model indicated that in the pessimistic EC irrigation water scenario, the WEFN index, CO2 emissions, fertilizer consumption, pesticide consumption, and gross margin would change by approximately +12%, −48%, −28%, −8%, and −74%, respectively, compared to the baseline scenario. Consequently, an increase in EC irrigation water, despite improving environmental conditions, would substantially diminish economic profit. Thus, overlooking the impact of EC irrigation water in the WEF nexus analysis could result in misleading conclusions.