Water engineering problems are typically nonlinear, multivariable, and multimodal optimization problems. Accurate water engineering problem optimization helps predict these systems’ performance. This paper proposes a novel optimization algorithm named enhanced multioperator Runge–Kutta optimization (EMRUN) to accurately solve different types of water engineering problems. The EMRUN’s novelty is focused mainly on enhancing the exploration stage, utilizing the Runge–Kutta search mechanism (RK-SM), the covariance matrix adaptation evolution strategy (CMA-ES) techniques, and improving the exploitation stage by using the enhanced solution quality (IESQ) and sequential quadratic programming (SQP) methods. In addition to that, adaptive parameters were included to improve the stability of these two stages. The superior performance of EMRUN is initially tested against a set of CEC-17 benchmark functions. Afterward, the proposed algorithm extracts parameters from an eight-parameter Muskingum model. Finally, the EMRUM is applied to a practical hydropower multireservoir system. The experimental findings show that EMRUN performs much better than advanced optimization approaches. Furthermore, the EMRUN has demonstrated the ability to converge up to 99.99% of the global solution. According to the findings, the suggested method is a competitive algorithm that should be considered in optimizing water engineering problems.