Planktonic oxygen isotope ratios off the Indus delta reveal climate changes with a multi-centennial pacing during the last 6 ka, with the most prominent change recorded at 4.2 ka BP. Opposing isotopic trends across the northern Arabian Sea surface at that time indicate a reduction in Indus river discharge and suggest that later cycles also reflect variations in total annual rainfall over south Asia. The 4.2 ka event is coherent with the termination of urban Harappan civilization in the Indus valley. Thus, drought may have initiated southeastward habitat tracking within the Harappan cultural domain. The late Holocene drought cycles following the 4.2 ka BP event vary between 200 and 800 years and are coherent with the evolution of cosmogenic 14C production rates. This suggests that solar variability is one fundamental cause behind Holocene rainfall changes over south Asia.