This study looks at aspects of the environmental health of the rural population in Timbío (Cauca, Columbia) in relation to the deterioration of water quality. The information was obtained through participatory research methods exploring the management and use of water, the sources of pollution and the perception of water quality and its relation to Helicobacter pylori infection. The results are part of the qualitative analysis of a first research phase characterizing water and sanitation problems and their relation to emerging infectious diseases as well as possible solutions, which was carried out between November 2013 and August 2014. The results of this research are discussed from an ecosystemic approach to human health, recognizing the complexity of environmental conflicts related to water resources and their impacts on the health of populations. Through the methodology used, it is possible to detect and visualize the most urgent problems as well as frequent causes of contamination of water resources so as to propose solutions within a joint agenda of multiple social actors.