The oceanic atolls and reef-complexes of the Archipelago of San Andres and Providencia exhibit semi-enclosed to rather open lagoon basins, where various characteristic bottom habitats occur. Certain areas of the lagoon floor are covered by sediments, being in some settings vegetated by algae or seagrass, and other areas by coralline framework of different types according to the composition and dominance of coral species and to their morphology and level of reef development. This study seeks to determine the spatial distribution patterns of lagoon bottom habitats based on the analysis of gradients of most relevant physical factors. Patterns in the occurrence and abundance of most habitats became evident in relation with wave-energy level, water depth, and the occurrence of islands. Some morphological reef types are oriented in a preferential direction and show spatial arrangements of development that are presumably related to prevailing current speed and direction and wave exposure.