For the last two decades, conflicts created by mining and their use of water has become an important issue for the Chilean geography. Several studies developed from Political Ecology perspective has constrained their analysis to the neoliberal period (post 1973). In this paper we follow a geo-historical standpoint, looking for a more complex understanding of the long period processes around mining and water. Through the analysis of different official documents (local reports/decrees and national laws) and scientific discourses (historical maps, papers and travel notebooks) of the 19th century, we have reconstituted the territorial genealogy of the Taltal region for the 1840-1900 period. We argue that the insertion of the Atacama Desert region (Northern Chile) into the world capitalist circuits of goods (minerals) push to the modernization of these territories (both in the 19th century). The profound territorial changes of this period, reconfigured the meanings and the material relations of the Taltal’s populations with water. In this way, discursive (scientific, political and legal) and material (investments and technology) processes transformed these "desert and unproductive" lands into a world scale mining territory, changing, at the same time, water into resource. Finally, we propose that a direct consequence of water modernization in Taltal region was the conflict between mining users and the invisibilisation of ancestral rationalities of water.