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Establishing scientifically the macro-location of a micropollutants monitoring network in tropical Andean rivers is a complex process, because information gathering is restricted by high-cost of analysis and limited availability of analytical techniques, which lead to inadequate sampling strategies that hinder the representativeness of samples. Thus, this work proposes a methodology for determining the number of representative sampling sections in a micropollutant monitoring network to characterise the ecological risk in tropical Andean torrential rivers. The proposed methodology consists of four stages: identification of the potential sampling units by Spline interpolation; calculation of the number of representative sections for a stratified sampling with an acceptable level of confidence and error; spatial allocation of the potential sampling units into sections by hierarchical cluster analysis; and representation of the spatial distribution of the sampling sections through a geographic information system (GIS). The proposed methodology is dynamic, and therefore, it can be revisited as more data are obtained in the subsequent years; it has the possibility of being applied to other inter-Andean valley rivers that interact with the tropical Andean sloppy mountains and serves as a tool for decision making by environmental authorities regarding the optimisation of the existing monitoring networks in terms of micropollutants to promote sustainable management of water resources. The proposed methodology is applied in the Upper Cauca River Basin (UCRB), which is located in southwest Colombia, South America.