Transboundary pollution is a major concern in environmental governance, partly driven by free-riding behaviors that generate boundary effects and are often inadequately addressed by existing policies. Although such effects have been widely documented in river and air pollution, their presence in nearshore seawater pollution remains unclear. It is also uncertain whether Marine Spatial Planning (MSP), which is designed to coordinate marine uses across jurisdictions, can effectively mitigate these effects. This study evaluates the effectiveness of the third round of China's MSP in managing transboundary nearshore seawater pollution. Using nearshore water quality data from 51 coastal cities between 2008 and 2021, we apply ordinary least squares regression to identify boundary effects in active phosphate and chemical oxygen demand. We then employ a difference-in-differences model to assess whether this round of MSP alleviated these effects. The results show that MSP did not mitigate boundary effects. Instead, it significantly intensified boundary-related pollution in terms of active phosphate and chemical oxygen demand. Further analysis based on planning scheme evaluation shows that conflict and intensity values positively moderate the boundary effect, suggesting that planning design and sea-use pressures play important roles in shaping transboundary pollution outcomes. The findings highlight the importance of geographical location in nearshore seawater quality and the necessity of comprehensive governance in transboundary marine area planning to mitigate transboundary environmental risks. Based on quasi-experimental evidence from China, this study provides insights for strengthening comprehensive coastal and bay-area planning in regions with decentralized environmental governance systems.