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Nutrient enrichment is a widely recognized threat to coastal coral reefs. Yet its impact on open ocean reefs is largely unknown due to the lack of long-term observations at remote sites and the entanglement of various environmental factors affecting coral growth. Here we determined growth rates and the carbonate chemistry of calcifying fluid (CF) of massive corals over the last 550 years at a remote South China Sea reef ecosystem. We show that large growth variations cannot be fully explained by changes in seawater pH or temperature due to the antiphase relationship between growth rate and pH cf as well as small sea surface temperature variations before the 1960s. Instead, coral growth rate decreases proportionally with past seabird populations over the past centuries. We suggest that excess nutrient loads through monsoon pumping and seabird migration played an important role in controlling coral growth at this remote reef ecosystem. Specifically, episodic eutrophication as indicated by a ∼ 3 per mil increase in coral δ13C has depressed coral growth by ∼30% during 15th to 18th centuries, which is comparable to the modern decline. Thus, accurate projections of future coral growth for remote reefs under ongoing human activities and climate change needs to take into account the history of past nutrient inputs into these ecosystems under pre-anthropogenic conditions, which has been overlooked previously due to a lack of historical observations. • Coral cores from an open ocean reef that grew from ∼1450 to present were analyzed. • Temperature affects multi-decadal variability in coral calcifying fluid DIC but not pH. • Reef-water pH modified by monsoon controls calcifying fluid pH and [CO 3 2−] • Eutrophication caused by monsoon and seabirds depressed coral growth during the Little Ice Age • An analog to the responses of corals to the projected rise in anthropogenic nutrient inputs. [ABSTRACT FROM AUTHOR]