Land use changes can have a significant impact on the terrestrial component of the water cycle. This study provides a comparison of three small headwater catchments in the Andean mountains of Colombia with different composition of land use. Several methods were used to quantify differences in the hydrological behavior of these catchments such as flow duration curves, stormflow analysis, and the linear reservoir concept. They were combined with an analysis of the characteristics of soils that contribute to understanding the aggregate catchment hydrological behavior. Andisols, which are soils formed in volcanic areas and with a large capacity to hold water, amplify differences in land use and limit the potential impact of land use management activities (conservation or restoration) on the water regulation function of catchments. Of the three studied catchments, less variability of flows was observed from the catchment with a larger percentage of area in forest, and a slower decrease of flows in the dry season was observed for the catchment with a relatively higher percentage of area in wetlands. Evidence is provided for the infiltration trade-off hypothesis for tropical environments, which states that after forest removal, soil infiltration rates are smaller and the water losses through quick flow are larger than the gains by reduced evapotranspiration; this is compatible with the results of the application of the linear reservoir concept showing a faster release of water for the least forested catchment.