Measuring chemical weathering histories in submarine fan deposits is critical if the impact of orogenic erosion on atmospheric CO2 levels is to be understood, yet existing records are often noisy and hard to interpret. In this study, we selected mudstones from two International Ocean Discovery Program (IODP) sites from the Indus submarine fan and carefully removed the biogenic carbonate. The resulting records of chemical weathering show two trends, one of reducing chemical alteration since ∼8 Ma and which is associated with the Indus River, while a second trend is linked to sediment delivery from peninsular India. The second trend shows little temporal variation. Sediment deposited at IODP Site U1456 in the central Laxmi Basin is preferentially, but not exclusively, Indus-derived, while that at Site U1457 on the eastern flank of Laxmi Ridge is more peninsula-derived. Both trends show much less variability than seen in earlier studies in which various grain-size fractions were integrated together. The efficiency with which CO2 is removed from the atmosphere during chemical weathering has decreased over time in the Indus River-derived material. This reflects both lower degrees of alteration in the sediment since the late Miocene and increasing derivation of sediment from Himalayan sources, rather than more mafic Karakoram-Kohistan rocks. Previous estimates of CO2 consumption have overestimated the contribution that the Indus Basin has made to reducing atmospheric CO2 by ∼28–68%. This work emphasizes the importance of analysing appropriate largely silt-sized sediment when considering submarine fan records and in rigorously removing biogenic carbonate.