Glaciers in the Arctic respond sensitively to climate change, recording the polar amplification of global warming with increasing mass loss. Here, we use glacier mass balances in Svalbard and northern Arctic Canada to categorize tropospheric variability and the associated summer circulation over the Arctic. We establish a link between annual glacier mass balances and their respective atmospheric forcings since 1950 using GRACE/GRACE-FO satellite data (2002–2021), as well as regional climate models and reanalysis data (1950–2019). We find that asynchronous behaviour of mass balance between the regions has become very likely since the early 2000s, exceeding the range of previous decadal variability. Related tropospheric circulation exhibits more meridional patterns, a greater influence of meridional heat advection and a wavier summer circulation. The traceable impact on glacier mass balances emphasizes the importance of dynamic next to thermodynamic climate changes for the future of glacier mass loss, Arctic ecology and societal impacts.