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The Holocene history of the continental margin of Belize has frequently been interpreted as being very straightforward, controlled almost entirely by postglacial sea level rise. Depending upon location, the dominant depositional environment, whether coral or mangrove, is either able to keep up with the rising sea level and thereby maintain its integrity through the present, or becomes drowned. Here we present sedimentary evidence from four mangrove cays situated on Turneffe Islands that shows an unusual pattern wherein early mangrove development is replaced by carbonate sedimentation before reverting back to mangroves in the relatively recent past. The bracketed carbonate layers, up to >2 m thick and resembling lagoon-floor material, display both a rough temporal coincidence across sites and a distinctive geographic signature, thinning landward irrespective of relative elevation. The carbonate sections are often underlain by a mixed sediment layer characterized by a jumble of stratigraphically incoherent mangrove clumps intermingled with carbonates. The replacement of mangrove peat with bottom-style carbonate deposition suggests a lowering of island surface elevation. Seismic activity is identified as the most likely cause, although hurricanes cannot be excluded. In either case the elevational reduction is probably amplified by peat collapse associated with mangrove mortality. The occurrence of such activity and the resulting catastrophic ecological/geomorphic change indicate a need for incorporating these geological perturbations in risk assessment for Turneffe Islands.