Ocean heat transport to marine terminating glaciers in Greenland exhibits interannual variability whose drivers remain incompletely understood. Using 2016–24 observations from Kangertittivaq, Greenland’s largest fjord system, we show that Atlantic Intermediate Water (AIW) that enters the fjord undergoes cooling throughout the fjord on interannual time scales, driven by advection of waters from the West Spitsbergen Current in Fram Strait. The strength of the subsurface inflow into Kangertertivarmit Kangertivat, the largest inner fjord branch, depicts distinct maxima in summertime, likely driven by entrainment of AIW into the meltwater plume of Daugaard-Jensen Glacier. Our study thus reveals that a superposition of large-scale advection and fjord meltwater dynamics facilitates the AIW cooling in the entire fjord system. We show that Kangertittivaq exhibits the same major AIW cooling event as 79N Glacier located 1000 km farther north, pointing to a common basin-scale forcing, synchronising ocean thermal conditions across a broad sector of the Greenland margin.