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A key consequence in climate change is the warming of deep waters, away from the faster warming rates of near-surface subtropical and tropical waters. Since surface and near-surface oceanic temperatures have been measured far more frequently in time and space than deep waters (>2000 m), deep measurements become quite valuable. Semi-enclosed basins, such as the Gulf of Mexico, are of particular interest as the waters below sills that connect with the neighboring oceans have residence times much longer than upper layers. Within the western Gulf of Mexico, near-bottom measurements at ~3500-m depths at four sites show a stable linear warming trend of ~16 ± 2 m°C decade−1 for the period 2007–18, and CTD data from eight oceanographic cruises occurring from 2003 to 2019 show a trend of ~18 ± ~2 m°C decade−1 from the bottom to ~2000 m below the surface. The bottom geothermal heat flux is a contributing factor to be considered in the warming and renewal of such waters, but it has not changed over millennia and is therefore unlikely to be the cause of the observed trend. The densest waters that spill into the Gulf of Mexico, over the Yucatan Channel sill, must mix substantially during their descent and in the near-bottom interior, losing their extreme values. A simple box model connects the observed warming, well within the Gulf interior, with that expected in the densest waters that spill from the North Atlantic into the Cayman Basin through Windward Passage and suggests that the source waters at the entrance to the Caribbean have been warming for at least 100 years. [ABSTRACT FROM AUTHOR]