Differences in soil water retention (SWR) characteristics between soil types and the factors driving those differences provide important information for land management, particularly in regions such as the Colombian Andes, which have limited water-storage infrastructure and where soils provide plant-available water and other ecosystem services. The objective of this study was to explore relationships between SWR and physical, chemical, and mineralogical properties of Andisols and Inceptisols through a case study of two watersheds in the Colombian Andes. This study identified a complex relationship between total carbon (TC), short-range order (SRO) minerals, and SWR. Both soil types had high SWR, with volumetric water content at permanent wilting point between 39% and 53%. Principal component analysis showed association of SWR with TC, SRO minerals, and % clay in both soil types. The Andisols of this study were coarse textured, allophanic (rich in allophane and imogolite — up to 17% in the B horizon), and with up to 15% TC in the A horizon. In contrast, the Inceptisols were fine textured (>30% clay) and higher in ferrihydrite than the Andisols. The formation of organo-metallic complexes was observed in A horizons; however, TC was lower under pasture than forest in both soil types. The addition of organic matter to soils with SRO minerals, such as the soils of this study, may foster the formation of organo-metallic complexes, stabilize soil C, and enhance SWR. Consequently, both study sites may benefit from management practices that increase soil organic matter.