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Excess anthropogenic phosphorus (P) supplied to marine systems, which may subsequently jeopardize ecosystem structure and function, has altered the P balance and quadrupled its flow. However, due to the diversity of P sources, the unpredictability and variability of human activities, and the absence of long‐term records, it remains uncertain how long the effects of excess P persist in aquatic ecosystems, and whether it stimulates gross primary productivity. In this study, we utilized geochemical proxies in coral skeletons from an atoll in the Xisha Islands of the South China Sea to reconstruct historical patterns of P in surface seawater. This atoll has remained in a natural state for an extended period of time, except for a short period of unambiguously documented guano extraction. Analyses of coral skeletons dating back to 1851 CE distinctly show that the P concentration in surface seawater increased abnormally in the 1960s. We deduced that guano extraction at that time led to an abrupt increase in the long‐term equilibrium of seawater P concentration. Subsequent P addition appeared to have continued for at least ~30 years after phosphorite exploitation ceased, and P showed a decay period that was longer than that of other elements. Similar temporal trends of coral P/Ca and δ13C indicated that elevated marine primary productivity was associated with increased P. Large inputs within a short period, as well as the continued influence of P over the long term, can serve as a natural ecological analog for coral reefs subject to nutrient contamination.

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