Tropical forests are globally important for their biodiversity and the ecosystem services, and they are key to the global water cycle. Anthropogenic changes and pressures affecting tropical forests affect the fundamental role of tropical forests in water supply. This study evaluates the relationship between the vegetation coverage in the high Andean forest of the “El Malmo” Protected Forest Reserve and the quality and quantity of intercepted runoff; the life zone analyzed comprises four types of cover: dense high Andean forest, low secondary vegetation, broadleaf plantation and mosaic of pasture with natural spaces. Eight setups (two per cover) were installed, each composed of a runoff plot and a precipitation meter under the canopy; data collection was carried out every eight days for 24 weeks. The results indicate that precipitation interception does not vary in each canopy, while surface runoff and its quality with respect to sediment are affected, which is mainly due to differences in soil physical conditions. The cover that allows the best dimensions of water quality and quantity is the dense high Andean forest. The influence of anthropic intervention in the area and the presence of invasive species negatively affect these variables. This work provides knowledge on the hydrological behavior of the reserve for forest management. It also generates information on the interception/runoff relationship in the forests of the Cundiboyacense region, which has not been available until now, becoming an starting point of comparison for further research in high Andean ecosystems.