Traditional villages hold significant historical and cultural value as the precious heritage of China’s agricultural civilization. Currently, against the backdrop of increasing urbanization and rapid expansion of urban construction land, the spatial patterns of traditional villages across various regions in China are being encroached upon and damaged, with protection pressures growing daily. As one of the important cradles of Chinese civilization, the Lower Yangtze River Basin (LYRB) has traditional villages closely linked with its water systems, forming a unique human-land relationship and spatial distribution pattern. However, influenced by the rapid urbanization process, the spatial patterns of traditional villages in this region also face a crisis, and the contradiction between protection and development is becoming increasingly prominent. How to balance this contradiction and ensure the reasonable protection and sustainable development of traditional villages has become an urgent issue to address. Therefore, this study focuses on the LYRB. Using ArcGIS tools and combined with mathematical analysis methods, the spatial distribution characteristics and essential influencing factors of traditional villages in this area were screened and analyzed. The objective was to examine the spatial structural relationship between traditional villages, four water system types, and nine sub-basin units, intending to reveal the unique interdependence between the water system and traditional villages in this area. This would provide scientific support for the formulation of scientific conservation strategies. The research results show that: (1) Traditional villages in The LYRB form two core clusters spatially and exhibit substantial spatial accumulation; (2) Water system characteristics are the main factors affecting the distribution of traditional villages; (3) In the LYRB, the spatial distribution of the nine sub-basins is closely related to the spatial distribution of traditional villages, resulting in typical regional spatial differentiation of traditional villages in this area. This study is based on a watershed perspective, and the results highlight the importance of the water system network in the development of traditional villages, revealing a unique spatial dependency relationship between traditional villages and the water network in the LYRB. In order to ensure the comprehensive protection of the traditional village system in this region, it is essential to adhere to the fundamental principles that govern its spatial configuration. A tripartite collaborative protection system based on the watershed should be formulated from the perspective of the overall distribution relationship between the water network and the traditional villages. This system would serve to protect the overall landscape, the water network pattern, and the traditional villages. Establishing an overall pattern view of integrating the water system network and the traditional villages is essential.