Typhoons regularly hit the coasts along the northern South China Sea during summer monsoon. However, little is known on the effects of typhoon-related heavy precipitation on estuarine dynamics and coastal ecosystems. We analyzed physico-chemical characteristics, and concentrations and composition of dissolved and suspended matter in the Wenchang/Wenjiao Estuary (WWE) on the tropical island of Hainan, China, prior to and after typhoon Kammuri in August 2008. Before the typhoon, the estuary displayed vertical and horizontal gradients. High nutrient inputs from agriculture and widespread aquaculture were to a large extent converted into biomass inside the estuarine lagoon resulting in low export of nutrients to coastal waters and a mainly autochthonous origin of total suspended matter (TSM). Heavy typhoon-associated precipitation increased river runoff, which moved the location of the estuarine salinity gradient seaward. It resulted in an export of dissolved and particulate matter to coastal waters one day after the typhoon. Dissolved nutrients increased by up to an order of magnitude and TSM increased approximately twofold compared to pre-typhoon values. Lower δ 13C org and δ 15N and elevated C/N ratios of TSM together with lower chlorophyll a (chl a) concentrations indicated an increased contribution of terrestrial material originating from typhoon-induced soil erosion. Local uptake of excess nutrients inside the lagoon was inhibited because of reduced water transparency and the lack of phytoplankton, which had been washed out by the initial freshwater pulse. Two weeks after the typhoon, TSM concentration and composition had almost returned to pre-typhoon conditions. However, physico-chemical properties and nutrients were still different from pre-typhoon conditions indicating that the estuarine system had not fully recovered. Unusually high chl a concentrations in the coastal zone indicated a phytoplankton bloom resulting from the typhoon-induced nutrient export. The typhoon-induced flushing of the WWE resulted in hyposalinity, reduced water transparency, siltation, as well as temporary eutrophication of coastal waters. These are physiological stressors, which are known to impair the performance of adjacent seagrass meadows and coral reefs. The predicted increase in typhoon frequency and intensity will lead to a frequently recurring exposure of coastal ecosystems to these threats, particularly in the South China Sea region where aquaculture is widespread and tropical cyclone frequency is at a maximum.