A high-resolution diatom record from site MD05-2908 in the Southern Okinawa Trough, East China Sea, reveals pronounced multidecadal- to centennial-scale palaeoceanographic changes throughout the last millennium. Summer sea-surface salinity (SSS) was reconstructed using a weighted averaging partial least squares diatom-based training set. The reconstructed SSS shows slightly decreasing values during the period AD 905–1930 with considerable fluctuations superimposed on this general trend. Relatively high-salinity conditions during the interval AD 905–1450 probably suggest a low flood frequency in north-eastern Taiwan. Furthermore, the high SSS values are associated with a strong and stable influence of the Kuroshio Current on the Southern Okinawa Trough during the Medieval Climate Anomaly. The period AD 1450–1930 is characterized by three low-salinity intervals (AD 1450–1500, AD 1625–1725 and AD 1770–1880) separated by periods of relatively high salinity. The low SSS intervals indicate increased freshwater discharge into the Southern Okinawa Trough during the Little Ice Age, probably as a result of higher flood frequencies in north-eastern Taiwan. Spectral and wavelet analyses suggest that this pattern was linked to multidecadal variations in summer SSS, presumably associated with the Pacific Decadal Oscillation. Copyright © 2012 John Wiley & Sons, Ltd.