The Yangtze River Basin is the largest river basin in China and has the most complex trans-boundary problems. The water quality monitoring system of the provincial boundary sections in the basin is the typical go-to system to show the interaction between administrative regions and basins. In this article, we discuss the water quality monitoring system in the basin from a legal perspective, explore the achievements and deficiencies of the system, and identify the main elements that constrain the effective operation of the system in the basin, including the fragmented competencies of monitoring institutions, the different monitoring techniques, the overlapping monitoring contents and scopes, the different data releasing channels, and the different applications of the data. We provide legislative suggestions to implement the newly enacted Yangtze River Protection Law and valuable lessons for the design of monitoring systems in other countries or (trans-boundary) basins that face a similar situation.