Multilayered karst systems of both above- and underground types were formed on the Yucatan Peninsula at the absolute heights from -150 m offshore to more than 2000 m in the surrounding mountains. Several floors of karst topography were identified: shelf (Mesoamerican Reef) with flooded caves and cenotes; coastal areas with shallow caves and cenotes and dense network of flooded tunnels; the transition zone – sloping plain with deeper cenotes, caves and rare tunnels; hilly northern central part with the rare deep cenotes and caves and polje; Peten plateau with fragments of dry valleys, polje, caves; hilly-low mountains framing with inselberg karst, caves and partially underground rivers; mountains with numerous waterfalls, systems of extremely deep caves, underground rivers, polje. Multi-floor structure of underground karst forms are mainly due to fluctuations of sea level: a periodic drainage of the territory and changes of erosion basis had led to incise of surface and underground watercourses. As a result karst process extended to the entire zone of active water exchange. The most rapid formation of cavities was in the areas of halocline fluctuations. Numerous fractured zones of different origins were a decisive in the rise, development and spatial features of karst systems.