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Tropical maritime precipitation affects global atmospheric circulation, influencing storm tracks and the size and location of subtropical deserts. Paleoclimate evidence suggests centuries-long changes in rainfall in the tropical Pacific over the past 2,000 y, but these remain poorly characterized across most of the ocean where long, continuous proxy records capable of resolving decadal-to-centennial climate changes are still virtually nonexistent despite substantial efforts to develop them. Here we apply a new climate proxy based on paired hydrogen isotope ratios from microalgal and mangrove-derived sedimentary lipids in the Galapagos to reconstruct maritime precipitation changes during the Common Era. We show that increased rainfall during the Little Ice Age (LIA) (similar to 1400-1850 CE) was likely caused by a southward migration of the Intertropical Convergence Zone (ITCZ), and that this shift occurred later than previously recognized, coeval with dynamically linked precipitation changes in South America and the western tropical Pacific. Before the LIA, we show that drier conditions at the onset of the Medieval Warm Period (similar to 800-1300 CE) and wetter conditions ca. 2 ka were caused by changes in the El Nino/Southern Oscillation (ENSO). Collectively, the large natural variations in tropical rainfall we detect, each linked to a multicentury perturbation of either ENSO-like variability or the ITCZ, imply a high sensitivity of tropical Pacific rainfall to climate forcings.