Prior to the establishment of the Dujiangyan water conservancy project, the Chengdu Plain had experienced prolonged flooding due to the Minjiang River. However, the prehistoric city site located within the Chengdu Plain, dating back 4 000 years, demonstrates that the ancestors of ancient Shu had already acquired techniques in flood management. Through spatial analysis of eight ancient city sites from the Baodun cultural period in the Chengdu Plain, this paper elucidates the relationships between ancient urban construction and water systems from macro, meso, and micro scales. Furthermore, it provides a detailed examination of structural measures to mitigate water-related disasters during urban development. Results indicate that the ancestors of ancient Shu had already developed the techniques of constructing elevated platforms, reinforcing city walls, excavating ditches, utilizing wooden bones and pebbles for water management, which were established more than 2 000 years before the advent of the Dujiangyan water conservancy project. This development significantly influenced the flood control technologies of subsequent generations. The concepts, principles, technologies, and methodologies of water management outlined in this study not only serve as a theoretical contribution to the understanding of prehistoric civilization in Chengdu but also offer theoretical and practical guidance for the contemporary construction of sponge city and the promotion of ecological civilization.