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Hypoxia impacts sediment nitrogen (N) cycling, yet its effects remain poorly constrained and exhibit strong cross-system inconsistency. We investigate these mechanisms through observations and mass-balance analysis of the Pearl River Estuary region, a typical estuarine coastal system under diverse environmental regimes. Our results show that low-oxygen conditions in the bottom waters increased sediment ammonium efflux. Under well-oxygenated bottom waters, 75% of the ammonium released from organic matter was oxidized within the sediments, with the remaining 25% entering the water column. Under low-oxygen conditions, ammonium efflux increased to 55% of that from organic matter, and only 45% of remineralized ammonium was oxidized through nitrification. With reduced sediment nitrification under hypoxia, denitrification decreased, removing only 53% of remineralized organic N in sediments compared to 76% under high bottom-oxygen conditions. This is because denitrification depends heavily on nitrate supply by nitrification, while nitrate concentrations in bottom waters were too low to support adequate nitrate influx to the sediments. Using a mass-balance analysis, we further demonstrate that this mechanism operates in many coastal systems with low-to-moderate nitrate levels. Thus, bottom-water hypoxia likely enhances sediment N recycling and reduces N removal on a broader scale, creating amplifying feedback to eutrophication in coastal N-limiting systems.