<p>Global commitments to water ecosystems protection are intensifying, with nations adopting increasingly diverse policy frameworks for improving aquatic sustainability. The establishment of effective transboundary governance mechanisms has emerged as a fundamental prerequisite for ensuring comprehensive protection of water ecosystems. However, this imperative is often weakened by the conflicting priorities of different governments, which inevitably results in strategic games between them. This study uses evolutionary game theory to model strategic interactions among Chinese jurisdictions sharing river and lake basins, integrating extensive field research with mathematical analysis. Our framework reveals two stable equilibria: a suboptimal non-cooperative state and an optimal collaborative equilibrium characterized by reciprocal protection efforts between regional governments. We develop a novel theoretical framework to analyze how extrinsic and intrinsic factors interact to reshape intergovernmental cost-benefit calculations in water ecosystems protection. For extrinsic factors, our analysis reveals that incentive and constraint mechanisms collectively determine governments’ willingness to invest in protection efforts. Properly designed incentive structures can overcome free-riding behavior, while binding constraints ensure minimum compliance standards. Three intrinsic factors emerge as critical determinants: governance paradigms, organizational interaction, and information transparency. These collectively reconfigure intergovernmental dynamics by fostering sustainability norms, improving interaction quality, and reducing information asymmetries, which creates an institutional environment conducive to sustained collaboration. By bridging game theory with real-world governance dilemmas, this work proposes a transferable framework for aligning local incentives with global water sustainability goals, offering policy-relevant insights for collaborative water governance.</p>