We report on epibenthic foraminiferal δ18O and δ13C and percentage coarse fraction records from Caribbean Ocean Drilling Program (ODP) Site 999 (12¿44'N, 78¿44'W, water depth 2828 m) spanning the interval from 8.5 to 5.3 Ma. Low epibenthic δ13C values and low amounts of sand-sized particles (mostly foraminifer shells) indicate a poorly ventilated deep Caribbean throughout the late Miocene. At this time the deep Caribbean was dominated by a nutrient-rich and corrosive water mass. A generally constant δ13C gradient between the Caribbean and deep Atlantic records during the late Miocene suggests that the fluctuations in δ13C reflect global changes in δ13C of the dissolved inorganic carbon due to varying erosion of organic carbon from terrigenous soils and shelf sediments. The observed 100-kyr cyclicity of epibenthic δ13C is in good accordance with the variability of terrigenous input to the equatorial Atlantic as recorded by magnetic susceptibility records of the Ceara Rise. However, some short-term gradient changes between 7.0 and 4.5 Ma indicate a poorer ventilation of the deep Atlantic related to a reduced production of deep water in the Atlantic. The Messinian Salinity Crisis between 6.0 and 5.3 Ma did not affect the intermediate to deep water gradient between the Caribbean and the Atlantic. Comparison to the Bahama platform record of ODP Site 1006, however, indicates a poorer ventilation of the shallower northern Caribbean basins coincident with the isolation of the Mediterranean Sea.