Geochemical cycles of trace metals are important influences on the composition and function of the marine ecosystem. Although spatial distributions of most trace metals have now been determined in at least some parts of the oceans, temporal variations have barely been studied on account of data limitations. In this paper, we report on a 159-year record of trace metal concentrations from a Porites coral from the northern South China Sea (SCS), and discuss how oceanic and climatic processes control variations in Mn, Cu, and V concentrations in this region. Our results show that trace metal concentrations in the coral skeleton demonstrate decadal to interdecadal fluctuations, and that their variations are controlled by different mechanisms. The input of Mn to reef water is partly controlled by the Pacific Decadal Oscillation (PDO), which controls precipitation and river runoff. Surface-water concentrations of the nutrient-like element Cu are controlled by summer upwelling to the east of Hainan Island. The concentrations of V show complex inter-relationships, and are linked to riverine input prior to the 1990 and to upwelling after the 1990. Our results imply that in the northern SCS, ocean-atmosphere climate fluctuations, such as the PDO and the East Asian Summer Monsoon (EASM), are important factors that influence long-term variability of Mn, Cu, and V concentrations in seawater, by controlling precipitation-related river runoff and the strength of upwelling systems. This article is protected by copyright. All rights reserved.