Paramos are high altitude Andean ecosystems in tropical South America. They are considered “water factories” because they provide water for 100 million people around the Andes. Their extraordinarily high capacity to regulate water depends on specific soil characteristics, such as high infiltration rates, high porosities, high organic matter (OM) contents, and low bulk densities. However, changes in native land covers for agriculture activities represents a threat for their efficiency in storing and regulating water flows. During a one-year survey we measured the infiltration rates, OM, organic carbon (OC), total nitrogen (TN), soil bulk density (SBD), and relative water content (RWC) across three native land covers (unmanaged shrubs [Diplostephium sp], cushion plants [Disterigma empetrifolium], and tussock grass [Calamagrostis effusa]) and three land uses (cattle grass [pasture], potato [Solanum tuberosum] crops, and managed shrubs [living fences]) in two watersheds in Paramo Paja Blanca in Colombia. The three land uses were changed from native land covers in 1985. Soils under cattle grass showed the most critical damages, such as compaction and OM, OC, and TN depletion, with worse values than any reported in previous publications. In comparison to native land covers, land uses showed on average 10-fold lower infiltration rates; three-fold lower OM, OC, and total N; two-fold lower RWC; and 18% higher SBD. Soils under potato crops didn't show different infiltration rates from native land covers, which is an artifact caused by the increase in porosity and the boost in vertical water movement by tillage. However, they showed lower SBD, OC, OM, and TN, and a lower capacity for water storage. These results point out the association between land cover and land use with soil properties and infiltration rates, which has been suggested from few previous studies in the Paramos. The interaction between vegetation cover and the physical-chemical soil status should be considered for land management and ecological restoration in Paja Blanca.