There is compelling evidence that episodic deposition of large volumes of fresh water into the oceans strongly influenced global ocean circulation and climate variability during glacial periods1,2. In the North Atlantic region, episodes of massive freshwater discharge to the North Atlantic Ocean were related to distinct cold periods known as Heinrich Stadials1–3. By contrast, the freshwater history of the North Pacific region remains unclear, giving rise to persistent debates about the existence and possible magnitude of climate linkages between the North Pacific and North Atlantic oceans during Heinrich Stadials4,5. Here we find that there was a strong connection between North Atlantic circulation changes during Heinrich Stadials and injections of fresh water from the North American Cordilleran Ice Sheet to the northeastern North Pacific. Our record of diatom 18O (a measure of the ratio of the stable oxygen isotopes 18O and 16O) over the past 50,000 years shows a decrease in surface seawater 18O of two to three per thousand, corresponding to a decline in salinity of roughly two to four practical salinity units. This coincided with enhanced deposition of ice-rafted debris and a slight cooling of the sea surface in the northeastern North Pacific during Heinrich Stadials 1 and 4, but not during Heinrich Stadial 3. Furthermore, results from our isotope-enabled model6 suggest that warming of the eastern Equatorial Pacific during Heinrich Stadials was crucial for transmitting the North Atlantic signal to the northeastern North Pacific, where the associated subsurface warming resulted in a discernible freshwater discharge from the Cordilleran Ice Sheet during Heinrich Stadials 1 and 4. However, enhanced background cooling across the northern high latitudes during Heinrich Stadial 3—the coldest period in the past 50,000 years7—prevented subsurface warming of the northeastern North Pacific and thus the increased freshwater discharge from the Cordilleran Ice Sheet. In combination, our results show that nonlinear ocean–atmosphere background interactions play a complex role in the dynamics linking the freshwater discharge responses of the North Atlantic and North Pacific during glacial periods.