Infiltration depends on the surface conditions of the soils, such as the surface covering of rock fragments and some of the properties of the matrix such as total porosity. Research reports inconclusive results regarding the influence of rock fragment cover on soil water infiltration that usually does not involve the spatial component in the analyses. The objective of this research was to spatially model the base infiltration rate and its relationship to rock fragment cover and the total porosity in soils of an Andean micro-basin. Hydrological response units were used to carry out stratified sampling in the basin. Infiltration was measured in the field using double ring infiltrometers. Surface rock fragment cover was estimated visually, and total porosity was determined using a tension table. Results showed that higher values in the rate of soil infiltration predominated on the slopes of the upper parts of the basin, while in the lower parts the values were lower. Infiltration had a logarithmic-exponential type distribution. The spatial autocorrelation model showed the best performance (r = 0.863) to model the relationship between the variables. This was the first research involving spatial modeling in the relationship between rock fragment coverage and soil infiltration, showing that infiltration was a spatially correlated variable related to changes in total porosity and soil coverage of rock fragments on the ground surface. This provided new information on the behavior of soils with rock fragments in tropical areas that have been little studied.