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The collapse of the Maya civilization in the late 1st/early 2nd millennium CE has been attributed to multiple internal and external causes including overpopulation, increased warfare, and environmental deterioration. Yet the role hurricanes may have played in the fracturing of Maya socio-political networks, site abandonment, and cultural reconfiguration remains unexplored. Here we present a 2200 yearlong hurricane record developed from sediment recovered from a flooded cenote on the northeastern Yucatan peninsula. The sediment archive contains fine grain autogenic carbonate interspersed with anomalous deposits of coarse carbonate material that we interpret as evidence of local hurricane activity. This interpretation is supported by the correlation between the multi-decadal distribution of recent coarse beds and the temporal distribution of modern regional landfalling storms. In total, this record allows us to reconstruct the variable hurricane conditions impacting the northern lowland Maya during the Late Preclassic, Classic, and Postclassic Periods. Strikingly, persistent above-average hurricane frequency between ~ 700 and 1450 CE encompasses the Maya Terminal Classic Phase, the declines of Chichén Itza, Cobá, and subsequent rise and fall of the Mayapán Confederacy. This suggests that hurricanes may have posed an additional environmental stressor necessary of consideration when examining the Postclassic transformation of northern Maya polities.