The Indonesian throughflow (ITF) is a chokepoint in the upper ocean thermohaline circulation, carrying Pacific waters through the strongly mixed Indonesian Seas and into the Indian Ocean. Yet the influence of the ITF on biogeochemical fluxes into the Indian Ocean is largely unknown. This study determines the first depth- and time-resolved nitrate, phosphate, and silicate fluxes at the three main exit passages of the ITF: Lombok Strait, Ombai Strait, and Timor Passage. Nutrient flux as well as its variability with depth and time differs greatly between the passages. We estimate the effective flux of nutrients into the Indian Ocean by accounting for existing nutrients in the basin and find it largest in the upper 300–400 m. This suggests that the majority of ITF nutrient supply to the Indian Ocean is to thermocline waters, where it is likely to support new production and significantly impact Indian Ocean biogeochemical cycling.