The Green Revolution rapidly increased India’s food production since the 1960s, but excessive synthetic fertilizer use caused severe environmental problems. Our spatially explicit analysis for 1970–2020 indicates an uneven distribution of the dramatic increase of surpluses of India’s soil N (4.3 to 21.6 Tg N/year) and P budget (0.4 to 3.3 Tg P/year): with high surpluses in e.g., Green Revolution (GR) and South-West (SW) regions, lower surpluses in e.g., North-West (NW) and even local deficits within some other states Nutrient surpluses were growing primarily through increased use of synthetic fertilizers, which resulted in declining nutrient use efficiency, high N and P losses and soil P accumulation, with large regional heterogeneity. Total N loss is determined by the surplus, through “holes in the pipe”, whereby the holes (loss pathways) differ in diameter, as determined by climate, crop, soil, terrain and management. Ammonia volatilization ranged from 16% of the N surplus (NC) to 45% (GR states), and denitrification losses from 50% (NC and SW) to 38% (GR) and 28% (NE). N loss via leaching ranged from 46% (NE), to 22–26% (GR and NC), and 16% (SW), and surface runoff losses between 2% (GR) and 9% (NC). In the period 1970-2020, our estimated soil P accumulation across India amounts to 290 kg P/ha, highest in SW followed by NE and GR states and lowest in NC. The SW region also has the highest surface runoff P loss (40% of its regional budget), followed by NC (53%), NE (34%), and GR (26%). Addressing these regional differences can help developing effective, targeted and region-specific nutrient management strategies while meeting India’s rising food demand.