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Sinkholes develop on carbonate landscapes when caves collapse and can subsequently become lake-like environments if they are flooded by local groundwater. Sediment cores retrieved from sinkholes have yielded high-resolution reconstructions of past environmental change, hydroclimate, and hurricane activity. However, our understanding of the internal sedimentary processes of these systems remains incomplete. Here, we use a multiproxy approach including sedimentology (stratigraphy, coarse-grained particle density, bulk organic matter content), micropaleontology (ostracods), and geochemistry (δ13C and δ2H on n-alkanoic acids) to reconstruct evidence for paleolimnology and regional hydroclimate from a continuous stratigraphic record (Emerald Pond sinkhole) in the northern Bahamas that spans the middle to late Holocene. Basal peat at 8.9 m below modern sea level documents the maximum sea-level position at ~ 8200 cal. yr BP. Subsequent upward vertical migration of the local aquifer caused by regional sea-level rise promoted carbonate-marl deposition from ~ 8300 to 1700 cal. yr BP. A shift in coarse particle deposition and ostracods at 5500 cal. yr BP suggests some environmental change, which may be related to one or multiple internal or external drivers. Sapropel deposition from ~ 1700 to 1300 cal. yr BP indicates a fundamental change in limnology to promote increased organic matter preservation, perhaps related to the regional cooling during the Dark Ages Cold Period. We find δ2H28 values are largely invariant from 7700 to 6150 cal. yr BP suggesting a generally stable hydroclimate (mean − 133‰, 1σ = 5‰). The shift to more depleted values (− 156‰, 1σ = 19‰) at ~ 6000–4800 cal. yr BP may be linked to a weakened (eastern displaced) North Atlantic Subtropical High. Nevertheless, additional local hydroclimate records are needed to better disentangle uncertainties from either internal or external influences on the resultant measurements.