A Miocene (Langhian–Tortonian, ca. 15–10 Ma) tropical ramp system exposed in southern Puerto Rico is characterized by shallow-water facies consisting of heterozoans, red algae, large benthic foraminifera (LBF), and corals, which occur as isolated corals, segment- and cluster-type reefs, and reworked accumulations. Photozoan association components are limited to corals (Montastraea, Porites, Goniopora, and Agaricia) and LBF (amphisteginids, soritids, gypsinids, miliolids) that have been documented to tolerate elevated nutrients, turbidity, and cooler water conditions. Similar shallow-water carbonate systems are found throughout the Caribbean, and this regional development is thought to have resulted from the well-documented upwelling in the Caribbean during the Miocene. Sea-level fluctuations also exerted a major control on facies distributions and shifts in the Puerto Rico ramp, including a vertical facies pattern that occurs in each of three sequences. Basal parts of sequences, deposited during sea-level rises, are dominantly composed of mollusks, echinoderms, red algae, LBF, bryozoans, and solitary corals that formed in low-energy seagrass-bed environments with local associated higher-energy shoal environments. Coral facies occur only in upper parts of sequences and formed in shallow-water, low- to high-energy environments closely associated with seagrass beds during late highstands and sea-level falls. A similar vertical facies pattern occurs in time-equivalent sequences elsewhere around the Caribbean. Strontium-isotope age data indicate two sequence boundaries reflecting sea-level falls formed at about 12.3 Ma and 11.1 Ma. Correlation with time-equivalent unconformities in other well-dated areas in the Caribbean and to sea-level lows on eustatic curves suggests a global signature for sequence development. The connection between the Caribbean and the Pacific along the Central American Seaway (CAS), impacted by local tectonic episodes and sea-level fluctuations during the Miocene, affected nutrient influx and upwelling in the Caribbean, which may be reflected in the vertical facies pattern in shallow-water carbonate sequences. Times of restricted connection during sea-level falls and lows resulted in reduced nutrients and upwelling, which may have been more conducive to coral development. Time-equivalent tropical carbonate systems in the Mediterranean and Indo-Pacific show similarities to those in the Caribbean, indicating influence of global processes (cooling, temperature gradients, oceanographic circulation). Differences between areas indicates the importance of local and regional controls, which in the Caribbean was dominantly the opening and closure of the CAS.