The deterioration of water quality worldwide is a serious environmental problem. Water managers still need operational tools to assess water issues and to inform water planning and decision-making. The aim of this article is to propose a 3-step methodological framework for assessing water pollution problems by combining a conceptual modeling tool (DPSIR) with the development of a quantitative model (Multi-Criteria Decision Model). This contribution provides a practical and flexible evaluation tool for conducting an integrated assessment of eutrophication and agrochemicals delivered to groundwater-dependent shallow lakes. It lays out action guidelines for decision-making environmental managers within the context of intermediate cities in developing countries. Forty-one indicators were identified to characterize the D-P-S-I compartments and for the multi-criteria model conceptualization. In this work, response options analysis consisted of evaluating and choosing water management instruments via a decision support tool. Two lake watersheds located in the peri-urban of two middle-size cities, in Argentina, were chosen to illustrate this methodological approach. The ensuing results allowed establishing a ranking of areas to prioritize, identifying a criteria and sub-criteria to focus on in order to set out action guidelines to minimize water pollution and eutrophication. These action guidelines are urgently needed in emerging countries, where financial, human resources and infrastructure are limited. The scarcity of such causes important implications regarding policy solutions for environmental issues. The implemented decision support tool in both lake watersheds provided a common basis for the understanding of the ongoing water pollution problems and a quantitative ranking (i.e., decision scores) for defining specific actions (responses) for human-induced stresses on such natural systems.