<p>This study investigates transboundary water pollution control mechanisms in river basins through an evolutionary game-theoretic lens under ecological compensation frameworks. Focusing on China's Qiantang River Basin, we construct a three-party evolutionary game model incorporating higher-level government, upstream (Chun'an County), and downstream (Jiande city) local governments to analyze strategic interactions in pollution governance. This research compares unidirectional and bidirectional ecological compensation mechanisms while considering hierarchical regulatory constraints. The results demonstrate that both compensation models achieve stable equilibrium when superior government oversight is incorporated, although bidirectional compensation results in superior synchronization in regional cooperation while potentially inducing regulatory complacency in superior governments. Local governments' benefit‒cost ratios and pollution-induced economic losses emerge as critical determinants of strategic stability, with bidirectional compensation showing greater resilience against cost fluctuations. Optimal incentive-penalty intensity from superior governments significantly accelerates collaborative governance convergence, requiring balanced calibration to maintain regulatory vigilance. Through numerical simulations parameterized with real-world hydrological and policy data, we demonstrate that bidirectional compensation enhances cooperative stability through reciprocal accountability mechanisms, particularly in managing land-based pollution affecting coastal marine environments. This study contributes to transboundary environmental governance by operationalizing vertical‒horizontal compensation synergies and providing evidence-based insights for China's evolving ecological compensation policies. Practical implications highlight the necessity of maintaining dynamic compensation standards, strengthening intergovernmental monitoring, and optimizing fiscal instruments for sustainable basin management.</p>