Western boundary currents (WBCs) have intensified and become more eddying in recent decades due to the spin-up of the ocean gyres, resulting in warmer open ocean temperatures. However, relatively little is known of how WBC intensification will affect temperatures in adjacent continental shelf waters where societal impact is greatest. We use the well-observed East Australian Current (EAC) to investigate WBC warming impacts on shelf waters and show that temperature increases are non-uniform in shelf waters along the latitudinal extent of the EAC. Shelf waters poleward of 32°S, are warming more than twice as fast as those equatorward of 32°S. We show that non-uniform shelf temperature trends are driven by an increase in lateral heat advection poleward of the WBC separation, along Australia’s most populous coastline. The large scale nature of the process indicates that this is applicable to WBCs broadly, with far-reaching biological implications.