AbstractThe Bahamian Archipelago has been the subject of extensive studies of stratigraphy, carbonate island morphology and diagenetic overprinting for many decades. A recently‐acquired dataset comprised of high‐resolution light detection and ranging, tightly spaced cored boreholes with image logs, thin sections, porosity and permeability measurements, and isotopic geochemical analyses provides a unique opportunity to perform detailed sequence stratigraphic analysis. This multi‐faceted study first establishes a new high‐resolution sequence stratigraphic framework for the Sandy Point area of San Salvador Island, encompassing six unconformity bound sequences (exposure surfaces) representing varying lengths of missing time. The stratigraphically lowest sequence is Late Pliocene in age and is dominated by reef facies capped by an extensive laminar caliche that represents 1.5 million years of exposure. The overlying Early Pleistocene is split into two sequences, EP1 and EP2, which are both dominated by low‐energy subtidal facies. The upper three sequences are tied to the Marine Isotope Stage 11, 9 and 5e interglacials, and are distinctly different in facies composition and architecture, being dominated by higher energy facies distributed in a more complex mosaic. The new stratigraphic framework highlights significant changes in depositional style and facies architecture that can be linked to increasing sea‐level amplitude oscillations and greater climate gradient at the Mid Pleistocene Transition. The well‐constrained framework is then used to provide key context for observed complex diagenetic evolution through repeated sea‐level inundation and subaerial exposure. These results suggest that well‐developed subaerial exposure surfaces drive increases in non‐matrix features in the subsequent stratigraphic package following exposure as the well‐cemented exposure surface acts to concentrate fluid flow and dissolution. Integration of non‐matrix features within this framework highlights the importance of dissolution/cementation patterns on formation of these modified unconformity surfaces for focusing later meteoric diagenesis and creating enhanced fluid flow pathways for continued multicyclic diagenetic events.