We evaluated the spatial and seasonal responses of precipitation in the Ganges and Brahmaputra basins as modulated by the El Niño Southern Oscillation (ENSO) and Indian Ocean Dipole (IOD) modes using Global Precipitation Climatology Centre (GPCC) full data reanalysis of monthly global land-surface precipitation data from 1901 to 2010 with a spatial resolution of 0.5° × 0.5°. The GPCC monthly total precipitation climatology targeting the period 1951–2000 was used to compute gridded monthly anomalies for the entire time period. The gridded monthly anomalies were averaged for the years influenced by combinations of climate modes. Occurrences of El Niño alone significantly reduce (88% of the long-term average (LTA)) precipitation during the monsoon months in the western and southeastern Ganges Basin. In contrast, occurrences of La Niña and co-occurrences of La Niña and negative IOD events significantly enhance (110 and 109% of LTA in the Ganges and Brahmaputra Basin, respectively) precipitation across both basins. When El Niño co-occurs with positive IOD events, the impacts of El Niño on the basins' precipitation diminishes. When there is no active ENSO or IOD events (occurring in 41 out of 110 years), precipitation remains below average (95% of LTA) in the agriculturally intensive areas of Haryana, Uttar Pradesh, Rajasthan, Madhya Pradesh, and Western Nepal in the Ganges Basin, whereas precipitation remains average to above average (104% of LTA) across the Brahmaputra Basin. This pattern implies that a regular water deficit is likely, especially in the Ganges Basin, with implications for the agriculture sector due to its reliance on consistent rainfall for successful production. Historically, major droughts occurred during El Niño and co-occurrences of El Niño and positive IOD events, while major flooding occurred during La Niña and co-occurrences of La Niña and negative IOD events in the basins. This observational analysis will facilitate well-informed decision making in minimizing natural hazard risks and climate impacts on agriculture, and supports development of strategies ensuring optimized use of water resources in best management practice under a changing climate.