To test the rate at which a lifeless but habitable environment (uninhabited habitat) can be colonized, artificial endolithic habitats were constructed in the laboratory and exposed to the natural environment. They were composed of sterile stacked sintered glass discs (stacks) containing CHNOPS elements, liquid water, energy and a carbon source, making them habitable for aerobic respiring organisms and phototrophs. One set of stacks was exposed fully to atmospheric conditions and one set was covered from direct overhead atmospheric input and precipitation. The process of colonization was heterogeneous across the stacks. After 3 months, all uninhabited habitats were colonized at all depths in both fully exposed and covered stacks. However, uninhabited habitable conditions persisted in covered stacks after 1 month, demonstrating the importance of the hydrological cycle in the connection between inhabited habitats and uninhabited habitats. Low porosity rocks were found to retard the extent of colonization compared with higher porosity rocks. Examination of genomic DNA demonstrated that the habitats were colonized by a community dominated by Proteobacteria. Covered stacks had a higher abundance of fungal sequences among eukaryotic colonizers. These data demonstrate the tight coupling between the appearance of habitable conditions and life and the reasons for the rarity of uninhabited habitats on the present-day Earth. On other planetary bodies, such as Mars, with more inclement atmospheres and less vigorous hydrological cycles or a lack of life, uninhabited habitats could persist for longer with consequences for the interpretation of data sent back by planetary science missions.