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13 pages, 4 figures, supporting Information https://doi.org/10.1111/ecog.05606.-- Data availability statement: Data available from the Dryad Digital Repository: https://dx.doi.org/10.5061/dryad.zs7h44j8s (Figuerola et al. 2021), Coastal hypoxia has become an increasingly acknowledged threat to coral reefs that is potentially intensifying because of increased input of anthropogenic nutrients. Almirante Bay (Caribbean Panama) is a semi-enclosed system that experiences hypoxia in deeper waters which occasionally shoals onto shallow coral reefs, suffocating most aerobic benthic life. To explore the long-term history of reefs in the bay we extracted reef matrix cores from two reefs that today experience contrasting patterns of oxygenation. We constructed a 1800-year-long record of gastropod assemblages and isotope compositions from six U-Th chronologically-constrained reef matrix cores. We extracted two cores from each reef at 3 m water depth and two additional cores from a deeper part (4.8 m) of the hypoxia-exposed reef. Results show that the deeper part of the hypoxic reef slowed in growth and stopped accreting approximately 1500 years BP while the shallow part of the reef continued to accrete to the present day, in agreement with a model of expanding hypoxia at this time. Our proxy-based approach suggests that the patterns of increasing herbivores and decreasing carbon isotope values in the deeper part of the hypoxic reef may have been driven by an increase in hypoxia via eutrophication caused by either natural changes or human impacts. Similar patterns in these paleoindicators occurred in the shallow part of the hypoxic reef during the last few decades. This suggests that the deep water hypoxia may be expanding to depths as shallow as 3 m and that shallow reefs are at greater risk due to increased human activity, This project and the research visit of BF to Texas A&M Univ. were financially supported by the Secretaría Nacional de Ciencia y Tecnología e Innovación (SENACYT; 47-2017-4-FID16-239), Sistema Nacional de Investigación (SENACYT), the Scholarly Studies Program (Smithsonian Institution), Smithsonian Tropical Research Institute (STRI), Texas A&M University and donations from M. Selin and family, J. Bilyk, V. and B. Anders, J. and M. Bytnar and the Young Presidents Organization (Los Angeles Gold Chapter). BF was supported by a STRI postdoctoral fellowship and the postdoctoral fellowships programme Beatriu de Pinós funded by the Secretary of Universities and Research (Government of Catalonia) and by the Horizon 2020 programme of research and innovation of the European Union under the Marie Skłodowska-Curie grant agreement no. 801370 (Incorporation grant 2019 BP 00183) and the Juan de la Cierva programme funded by the Ministry of Science and Innovation (Incorporation grant IJCI-2017-31478). With the institutional support of the ‘Severo Ochoa Centre of Excellence' accreditation (CEX2019-000928-S)