In Latin America, water resource management in some areas is difficult when all parts of a system are not considered (including its dynamism). Therefore, it becomes necessary to prepare instruments that facilitate management using a comprehensive approach. This study aimed to develop a methodology that allows one to conduct a prospective analysis of water management over delimited territories. The Zamora Huayco basin was chosen as the study area. This work included a survey of physical-natural, socioeconomic, and political-institutional variables, as well as a system structural analysis. Also, the generation of future scenarios and the strategic and tactical orientation for the integrated management of water resources. The results show that, of the 23 variables used, 19 were classified as key system variables. Most of the variables had strong impacts on each other, but at the same time these were highly receptive to changes. The behavior of change, proposed for the different uses and land cover in the basin for 2029, was considered as the objective scenario, highlighting the gain in forest areas and shrub vegetation. The strategic plans proposed in this methodology consider the structuring and collecting information in a single repository, creating communication channels between stakeholders and decision-makers.