Thermal discharge from power plants causes significant concerns in aquatic environments. The purpose of this study is to evaluate how river mouth morphodynamics, particularly spit development and removal, influence the dispersion of thermal plumes. To achieve this, a case study was carried out at a coastal power plant in southwest Türkiye, where thermal effluent is conveyed to the sea through a low-flow river. Field measurements combined with numerical modeling were used to analyze plume dynamics under varying spit configurations. Results revealed that the evolution of a spit on one side of the river mouth influences plume dispersion and redirects the mixing zone toward the opposite shoreline. Numerical simulations demonstrated that spit development reduces dispersion efficiency (by over 75%), while the physical removal of the spit significantly improves it, reducing temperature excess from 4–5 °C to 0–1 °C within the mixing zone, meeting safe environmental standards. The findings highlight the pivotal role of morphological changes in governing thermal discharge behavior and emphasize the importance of continuous monitoring and management strategies, such as periodic dredging, to ensure compliance with environmental regulations.