River systems in the Himalaya have been studied extensively to understand the processes driving periodic river valley aggradation and incision resulting due to rainfall, high relief, and ongoing deformation. When climatic forces are considered, the debate continues on whether wetter climatic intervals with localized glacier melting promote river aggradation through increased discharge and enhanced sediment load, or instead, it is during drier conditions that aggradation occurs through increased sediment to water ratio. This study, for the first time, attempts to constrain discharge during periods of established river aggradation and incision over late Quaternary. Here, geometric data from imbricated gravels of channel fills are used to calculate paleodischarges during net river aggradation at 47–23 ka, and preserved slack water deposits (SWDs) at 14–10 ka are used to constrain paleodischarges that occurred during net river incision. Catchment area-normalized discharge derived from these valley fill sequences ranges from 0.78 to 3.26 (×10−7 m s−1). Syn-incision discharge estimates yielded normalized discharge values of 6.17 (×10−7 m s−1) are considerably higher than discharges estimated from periods of aggradation. Morphometric analysis, chi slope, and Ksn, along the Indus River, observed no relation with the paleodischarge. This case study implies that net river incision in the upper Indus River occurs predominantly during relatively wetter climatic conditions than the climate during aggradation.