<p>The design of a micropollutant monitoring network in rivers is a challenging task because of the lack of environmental regulations, high laboratory analysis costs, and the limited availability of standardized analytical techniques, especially in Latin America. These constraints hinder the ability to make informed, data-driven decisions. In this study, we proposed a methodology that updates the micropollutant measurement process in rivers and incorporates a height variable to improve the precision of ecological threat index (hazard quotient) interpolations at unsampled sites using the cokriging method. The methodology is applied to a section of the Cauca River, the second most important river in Colombia. The sampling design is based on the stratification of sampling subsections, defined by geographic stratum similarity, enabling a more efficient placement of sampling stations at the macrolocation level. This approach not only improves the spatial representativeness of the data but also helps reduce measurement costs, an important aspect in regions with limited resources. In addition, the proposed methodology is dynamic and can be updated with new measurements, guaranteeing its sustainability over time and its applicability in surface water bodies (basins and rivers) with similar characteristics.</p>