The aim of this study is to improve the performance of the shuffled complex evolution (SCE) algorithm used in the optimization of hydropower generation in reservoirs as a complex issue in water resources. First, the SCE algorithm is merged with the differential evolution (DE) algorithm to form the SCE-DE algorithm. Then, a complex mathematical function is used as a benchmark to evaluate the performance and validate the SCE-DE algorithm and the outcomes are compared with the original SCE algorithm to show the superiority of the proposed SCE-DE algorithm. In addition, the two-reservoir system of Dez-Gotvand is considered as a real optimization problem to evaluate the performance of the SCE-DE algorithm. It is revealed that optimization by SCE-DE is much better than SCE. In conclusion, the results show that the proposed SCE-DE algorithm is a reasonable alternative to optimizing resource systems and can be used to solve complex issues of water resources.