We use geochemical data from a sediment core in the shallow-silled and intermittently dysoxic Kau Bay in Halmahera (Indonesia, lat 1°N, long 127.5°E) to reconstruct century-scale climate variability within the Western Pacific Warm Pool over the past ~3500 yr. Downcore variations in bulk sedimentary δ15N appear to reflect century-scale variability in basin ventilation, attributed to changes in oceanographic conditions related to century-scale fluctuations in El Niño Southern Oscillation (ENSO). We infer an increase in century-scale El Niño activity beginning ca. 1700 yr B.P. with peaks in El Niño activity ca. 1500 yr B.P., 1150 yr B.P., and ca. 700 yr B.P. The Kau Bay results suggest that there was diminished ENSO amplitude or frequency, or a departure from El Niño–like conditions during the Medieval Warm Period, and distinctive, but steadily decreasing, El Niño activity during and after the Little Ice Age.