Abstract Nutrient dynamics were studied in the estuary of the Wanquan River, a tropical mountainous river system of Hainan Island, China, during 2006–2009. The nutrients measured included NO3−, NO2−, NH4+, PO43−, Si(OH)4, total dissolved nitrogen (TDN), total dissolved phosphorus (TDP), dissolved organic nitrogen (DON), and dissolved organic phosphorus (DOP). The Wanquan River showed great variation in nutrient levels, was enriched in dissolved inorganic nitrogen (DIN) and dissolved silicate, and depleted in PO43−. The levels of dissolved silicate were higher than average for tropical systems. As a consequence the DIN:PO43− and Si(OH)4:DIN ratios were higher than the Redfield ratio. DON accounted for 18% of TDN in the Wanquan River, and DOP represented approximately 61% of TDP. Nutrients in the Wanquan River estuary behave either conservatively or nonconservatively. Nutrient biogeochemistry in the estuary is affected by human activities in adjacent areas and heavy rainfall associated with typhoons. Phosphorus may be the potential limiting nutrient for phytoplankton growth. A simple steady-state box model showed that riverine input was the major source of nutrients to the estuary, which acted as a source of all nutrients except dissolved silicate, TDP, and DOP. The results indicate that substantial quantities of nitrogen and PO43− are transported to the coastal system, and suggest that dissolved silicate accumulates in the sediment or is transformed into other forms.