This study aimed to quantitatively evaluate the performance of practical alternatives in modernization projects of surface water distribution systems in irrigation networks based on the water-food-energy nexus using the AHP-Entropy-WASPAS technique. Three methods of improved manual operation, decentralized automatic operation, and centralized automatic operation were developed under normal and water shortage operation scenarios and modeling the current status of water distribution in the main canal of the Isfahan Rudasht irrigation network as a case study. Water-based indicators (i.e., surface water delivery, surface water productivity, and surface water economic productivity), energy-based indicators (i.e., energy consumption, energy productivity, and economic energy productivity), and food-based indicators (i.e., food productivity and food economic productivity) were used to develop the nexus evaluation framework. The results showed that the average values of the water-food-energy nexus index in the manual operation method were estimated at 0.49 and 0.16 under normal and water shortage operation scenarios, respectively. These average values were estimated at 0.53 and 0.17 under normal and water shortage operation scenarios, respectively, by improving the method to the improved manual operation method. The decentralized automatic operation method improved these average values to 0.82 and 0.39 under normal and water shortage operation scenarios. Finally, using the centralized automatic operation method, these average values were 0.94 and 0.35 under normal and water shortage operation scenarios. Since the downstream secondary off-takes of the irrigation network receive no water even by upgrading the surface water distribution system to the decentralized automatic operation method under the water shortage operation scenario, it can be said that the performance of the centralized automatic operation method is more efficient than the decentralized automatic operation method due to the fair and uniform distribution of water in both normal and water shortage operation scenarios.