Here we present interannual rare earth element (REE) records spanning the last two decades of the 20th century in two living Porites corals, collected from Longwan Bay, close to the estuarine zones off Wanquan River of Hainan Island and Hong Kong off the Pearl River Delta of Guangdong Province in the northern South China Sea. The results show that both coral REE contents (0.5–40 ng g⁻¹ in Longwan Bay and 2–250 ng g⁻¹ in Hong Kong for La–Lu) are characterized with a declining trend, which are significantly negative correlated with regional sea-level rise (9.4 mm a⁻¹ from 1981 to 1996 in Longwan Bay, 13.7 mm a⁻¹ from 1991 to 2001 in Hong Kong). The REE features are proposed to be resulted from seawater intrusion into the estuaries in response to contemporary sea-level rise. However, the tendency for the coral Er/Nd time series at Hong Kong site is absent and there is no significant relation between Er/Nd and total REEs as found for the coral at Longwan Bay site. The observations are likely attributed to changes of the water discharge and sediment load of Pearl River, which have been significantly affected by intense human activities, such as the construction of dams/reservoirs and riverbed sediment mining, in past decades. The riverine sediment load/discharge ratio of the Pearl River decreased sharply with a rate of 0.02 kg m⁻³ a⁻¹, which could make significant contribution to the declining trend of coral REE. We propose that coastal corals in Longwan Bay and similar unexplored sites with little influences of river discharge and anthropogenic disruption are ideal candidates to investigate the influence of sea-level change on seawater/coral REE.