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Estuaries are areas of both freshwater and seawater that are partially enclosed with contact to the open sea and a flow of fresh water. Although the Jiulong River Estuary has a relatively small catchment, this area was found to exhibit high nutrient fluxes. The nutrient fluxes showed obvious fluctuations for different years. The Jiulong River Estuary was predominantly P-limited, and was slowly moving towards higher DIN:DIP and DSi:DIP ratios as the nitrate concentrations increased. The high nutrient fluxes into the estuary may affect estuarine ecosystems by the alteration of DO concentrations in bottom waters, causing harm to benthic fauna due to a lack of oxygen, triggering algal blooms. Additionally, the Jiulong River Estuary was slowly moving towards lower DSi:DIN and DSi:DIP ratios along with the change of time scales, which caused nutrient limitation of phytoplankton growth as P and Si levels decreased and became more limiting. [ABSTRACT FROM AUTHOR]