We present late Quaternary records of metastable carbonate dissolution determined for sediment cores recovered from intermediate water depths on the Nicaragua Rise (Caribbean Sea, 1000–1894 m) and near the Bahama Banks (western North Atlantic Ocean, 655 and 1934 m). Upper North Atlantic Deep Water is believed to dominate these two regions at present. Both areas are predicted to be good locations to study past variations of average middepth Atlantic chemistry and circulation. However, statistical analyses of metastable carbonate dissolution indices (% Mg calcite, pteropod abundance, % whole pteropods, and % clear pteropods) yielded a composite dissolution index (CDI) which displays different carbonate dissolution histories for Bahama and Nicaragua Rise sediments. The Bahama records resemble deep Atlantic carbonate records with dissolution during glacial oxygen isotope stages 6 and 4 and with preservation during interglacial stages 5 and 1. We observe two dissolution patterns at intermediate water depths of the Caribbean. The “deep” intermediate water pattern (1200–1894 m) resembles deep Caribbean carbonate records with dissolution during interglacial periods and preservation during glacial intervals. The “shallow” intermediate water record (<1200 m) resembles at times the Bahamas record and at other times the deep Caribbean record. These CDI records suggest that different water masses occupied the intermediate depth western North Atlantic and Caribbean during much of the late Quaternary. Observed differences between these regions may be related to variations in the flow of nutrient-rich, low CO3= Antarctic Intermediate Water through the Caribbean or to changes in the ventilation rate of equatorial thermocline and intermediate waters. These water-mass variations have influenced Caribbean carbon chemistry from the base of the thermocline down to abyssal water depths and may have had a significant effect on North Atlantic circulation and nutrients.