Abstract: Taking the evolutional relationship among “space of watershed”, “space of places” and “space of flows” as the theoretical foundation, this article explores the rapid deterioration of the river basin ecology and river health in Guangdong Province since the reform and opening up. Through reviewing the urban development along the river basins, it reveals the coupling development between traditional “local space” and “space of watershed” in the early stage. However, the new-type “space of places” dominated by the global “space of flows” has been separated from the “space of watershed” after the reform and opening up. In this process, the “space of flows” has strengthened the social and economic relationship between the Pearl River Delta and the world, but it has also damaged the ties between people and the river basins where they’re living. As a result, the man-land relationship has shifted from dependence to overriding utilization, which is the deep reason for the deterioration of the natural ecological environment in the river basins and rivers. Therefore, this article proposes to promote innovation in the regional spatial governance from two aspects: First, optimize the “dual evaluation” mechanism in the territory spatial planning by changing the ways of building the “space of places”, taking “watershed zoning” as the prerequisite in making a regional economic spatial development strategy. Second, take full institutional advantages of the “river and lake chief system” to promote multiple-goal river governance by strengthening departmental coordination.