Moisture transport from the Atlantic to the Pacific ocean across Central America leads to relatively high salinities in the North Atlantic Ocean1and contributes to the formation of North Atlantic Deep Water2. This deep water formation varied strongly between Dansgaard/Oeschger interstadials and Heinrich events-millennial-scale abrupt warm and cold events, respectively, during the last glacial period3. Increases in the moisture transport across Central America have been proposed to coincide with northerly shifts of the Intertropical Convergence Zone and with Dansgaard/Oeschger interstadials, with opposite changes for Heinrich events4. Here we reconstruct sea surface salinities in the eastern equatorial Pacific Ocean over the past 90,000 years by comparing palaeotemperature estimates from alkenones and Mg/Ca ratios with foraminiferal oxygen isotope ratios that vary with both temperature and salinity. We detect millennial-scale fluctuations of sea surface salinities in the eastern equatorial Pacific Ocean of up to two to four practical salinity units. High salinities are associated with the southward migration of the tropical Atlantic Intertropical Convergence Zone, coinciding with Heinrich events and with Greenland stadials5. The amplitudes of these salinity variations are significantly larger on the Pacific side of the Panama isthmus, as inferred from a comparison of our data with a palaeoclimate record from the Caribbean basin6. We conclude that millennial-scale fluctuations of moisture transport constitute an important feedback mechanism for abrupt climate changes, modulating the North Atlantic freshwater budget and hence North Atlantic Deep Water formation.