Surface soil moisture is an important hydrological parameter in agricultural areas. Periodic measurements in tropical mountain environments are poorly representative of larger areas, while satellite resolution is too coarse to be effective in these topographically varied landscapes, making spatial resolution an important parameter to consider. The Las Palmas catchment area near Medellin in Colombia is a vital water reservoir that stores considerable amounts of water in its andosol. In this tropical Andean setting, we use an unmanned aerial vehicle (UAV) with multispectral (visible, near infrared) sensors to determine the correlation of three agricultural land uses (potatoes, bare soil, and pasture) with surface soil moisture. Four vegetation indices (the perpendicular drought index, PDI; the normalized difference vegetation index, NDVI; the normalized difference water index, NDWI, and the soil-adjusted vegetation index, SAVI) were applied to UAV imagery and a 3 m resolution to estimate surface soil moisture through calibration with in situ field measurements. The results showed that on bare soil, the indices that best fit the soil moisture results are NDVI, NDWI and PDI on a detailed scale, whereas on potatoes crops, the NDWI is the index that correlates significantly with soil moisture, irrespective of the scale. Multispectral images and vegetation indices provide good soil moisture understanding in tropical mountain environments, with 3 m remote sensing images which are shown to be a good alternative to soil moisture analysis on pastures using the NDVI and UAV images for bare soil and potatoes.