Ecosystem services provide many benefits to society. These services have been classified into four categories: provisioning services, regulating, cultural and support. One of the major gaps in mapping these services is related to the lack of a standardized methodology that integrates biophysical and perceptual variables derived from the vision of relevant actors in a territory. Multi-criteria spatial analysis (MCSA) is an appropriate methodological framework to integrate this type of information. The present study aims at proposing and applying a methodology of multi-criteria analyses based on GIS tools and homogeneous environmental units (HEU) for mapping ecosystem services in Quepe river basin. Results indicated that provision, regulation and cultural services were significantly associated with the HEU Bosque Nativo. Furthermore, the level of presence of these services was significantly lower in the HEU Plantación and Tierras Agrícolas. We conclude that the method has the advantage of providing ease and flexibility in data spatialization, while collecting perceptual values of a specific service in the sub-basin.