In the context of ecological protection and high-quality development strategies within the Yellow River Basin, leading enterprises encounter challenges such as high governance costs and low economic returns while simultaneously fulfilling their distinct social responsibilities related to water ecological management. The reward and punishment policies implemented by the central government play a crucial role in shaping enterprises governance decisions and their subsequent outcomes. Nevertheless, existing research lacks a systematic analysis of the dynamic interplay between central government incentives, the commitment of leading enterprises to fulfill specific social responsibilities, and the effectiveness of water ecological governance. This study adopts a project portfolio perspective to develop a dynamic impact model that integrates multi-stage strategic periods, linking central government incentives and sanctions with leading enterprises fulfillment of special social responsibilities and governance outcomes. A two-layer nested multiple cluster genetic algorithm is employed to solve this model. The findings indicate that there exists an inverted “U” shaped relationship between the intensity of central government incentives/sanctions and governance effectiveness. Both excessive rewards and punishments may result in diminished governance outcomes. Furthermore, the project portfolio strategies employed by enterprises at various strategic stages are significantly shaped by the intensity of these incentives/sanctions. Additionally, the leading enterprises often engage in only the most basic forms of social responsibilities during the early stages of strategy implementation. This approach serves to mitigate potential penalties while allowing them to focus on high-return projects in subsequent stages, thereby maximizing the overall rewards. This research provides policy recommendations designed to optimize incentive/sanction mechanisms, reinforce assessment supervision, and enhance the capabilities of corporate governance. These suggestions provide theoretical foundations and practical guidance for central governments in formulating incentive policies aimed at water ecological management as well as assisting enterprises in refining their governance decision-making processes.