Uplift of mountains driven by tectonic forces can influence regional climate as well as regional drainage patterns, which in turn control the discharge of eroded sediment to the ocean. But the nature of the interactions between tectonic forces, climate and drainage evolution remains contested. Here we reconstruct the erosional discharge from the Indus river over the past 30 million years using seismic reflection data obtained from drill core samples from the Arabian Sea and neodymium isotope data. We find that the source of the Indus sediments was dominated by erosion within and north of the Indus suture zone until five million years ago; after that, the river began to receive more erosional products from Himalayan sources. We propose that this change in the erosional pattern is caused by a rerouting of the major rivers of the Punjab into the Indus, which flowed east into the Ganges river before that time. Seismic reflection profiles from the Indus fan suggest high mass accumulation rates during the Pleistocene epoch partly driven by increased drainage to the Indus river after five million years ago and partly by faster erosion linked to a stronger monsoon over the past four million years. Our isotope stratigraphy for the Indus fan provides strong evidence for a significant change in the geometry of western Himalayan river systems in the recent geologic past.