In Yucatán very shallow (30 cm), rocky and stony soils that dominate the landscape are underlain by limestone. Using a freshly exposed wall in a limestone quarry, we identified three main limestone strata (at the 0-2.5, 2.5-5 and, 5-7 m depths). Ground water is encountered at the 9-m depth and vegetation is a 10-year old deciduous forest. The upper layer, where the rock is hard, roots grow along holes, cracks, and crevices. On the middle layer roots grow also within the matrix of the soft limestone. We did not find any roots growing in the bottom layer. Therefore, we hypothesize that the vadose zone limestone has soil-like properties that support tree growth in Yucatán. In this study we analyzed the density, porosity, water holding capacity, mineralogy and micromorphology of those rocks to find out their potential relevance to root development and water storage. All the rocks were composed mainly of calcite but differed with respect to density, porosity and water-holding capacity as well as pore size and presence of fossils. Particle density was about the same whereas bulk density was highly variable among the rocks from the three layers. Porosity increased with depth as water-holding capacity and field water content increased during the dry season. We found roots associated with the different rock strata, most of them infected by mycorrhizal fungi. The top limestone layer is highly restrictive to roots, but roots that can reach lower layers find microsites and available water conducive to growth. The cracks and crevices are important features of the limestone because soil accumulates there providing sources of nutrients for roots at deeper sites. Since limestone does not represent a source of nutrients for plants, we suggest that mycorrhizal fungi associated with roots within rocks are facilitating plant water uptake.