Integrated land-sea development and protection are important for the sustainable development of coastal areas. To promote the transition from separate land-sea management to integrated land-sea governance, the scientific delineation of the integrated spatial zoning units of coastal watershed-nearshore waters is an important tool for integrated land-sea management. From the perspective of physical geography, this study uses digital hydrological analysis based on DEM data to determine the coastal basin range and generate multilevel watersheds and river networks using different thresholds, and establishes spatial correspondence among physical geospatial spaces, such as watershed zones, coastlines, and nearshore waters, after considering the boundaries of major estuaries and bays. On this basis, the coastal zone is divided into several integrated spatial zoning units of coastal watershed-nearshore waters, and a physical geography-based integrated spatial zoning method is developed to form a physical geography-based land-sea integrated spatial zoning scheme. This study conducted spatial heterogeneity research of the integrated spatial zoning units, from the perspectives of topography analysis, land use analysis, socioeconomic analysis of the watershed, sea use analysis, seawater quality analysis of the nearshore waters, and load pressure analysis of the watershed-nearshore waters. The elemental differences of zoning units are studied in detail, which can provide a data reference for establishing the relationship between watersheds and nearshore waters. Applying this research method to the Guangxi Zhuang Autonomous Region in China, where the land-sea linkage pattern is forming, can provide a spatial reference and scientific basis for land-sea integrated management for ecological protection and sustainable resource utilization in the coastal zone.