The historical urban fabrics are the evidence of traditional knowledge and practices generated by urbanization processes that take advantage of the morphological characteristics of the territory, ensuring a good balance between human settlement and natural environment. The Sassi of Matera, located on the slopes of the Gravina Stream along the two old streams of the Grabiglioni, or Fossi, represents an emblematic example of a resilient historical city. For centuries in the Sassi, the natural watercourses of the Grabiglioni provided the surface runoff collection to the Gravina Stream, ensuring the ecosystem balance and avoiding critical conditions such as uncontrolled surface runoff or flooding within the two urban districts of Sasso Barisano and Sasso Caveoso. In Matera as in many other cities, the most recent building expansions outside the historical centres and the transformations produced on the historical heritage have led to the alteration of these balances causing critical consequences. This study proposes an interdisciplinary investigation approach that analyse the transformations produced on the historical water infrastructure of the Grabiglioni and their urban context over time in order to understand the effects of these changes on the environment dynamics. The proposed investigation develops watersheds analysis that allows us to understand the interrelations between historical urban fabric and hydromorphic characteristics of the territorial context. This contribution proposes an integrated workflow that lays the foundations necessary for further research on the topic and for the recovery and enhancement of this heritage reproducible in other similar case studies.