Maize is one of the important cereal crops grown in rainfed regions of northwestern Himalayas, however, persistent use of chemical fertilizers coupled with poor soil nutrients and water holding capacity due to coarse textured soils poses serious threat to sustaining maize yield and soil health. To address these bottlenecks, a long-term experiment with application of organic manures and mineral fertilizer provides insights to quantify changes in soil organic carbon (SOC), crop yield and rain water use efficiency (RWUE) in rainfed area having low water use efficiency. A twelve years field experiment was conducted under dry sub-humid Inceptisols in northern India to study the potential impacts of organic and mineral fertilization on maize (Zea mays L.) productivity, water use efficiency and soil quality. Ten treatments were assessed, involving different nitrogen levels (20, 30, and 40 kg N ha⁻¹) combined with 10 tha⁻¹ year⁻¹ of farmyard manure (FYM), in-situ green manure from sunhemp, and the incorporation of Leucaena leucocephala leaves at 5 tha⁻¹ year⁻¹, including an unfertilized control. Maize yield increased linearly with increasing nitrogen application rates. The combination of FYM @ 10t ha−1 and 40 kg N ha−1(T4) yielded the highest maize production. Manure addition improved soil organic carbon (SOC) and major soil nutrients (N, P and K) while unfertilized control showed decline in soil nutrients compared to their initial values. Compared with control, incorporation of 10 t ha−1 FYM increased SOC by 1.3, 1.41, 1.44 times at application rate of 20, 30, 40 kg N ha−1, respectively. Application of N@40 kg ha−1 + 10t FYM ha−1 showed highest rain water use efficiency (RWUE) and relative production efficiency index (RPEI) (2.74 kg ha−1 mm−1 and 82, respectively) and the lowest rank sum of 6. Highly significant positive relationship existed between RPEI and RWUE, RPEI and sustainability yield index (SYI), RWUE and SYI indicated the superiority of FYM in combination with mineral fertilizer. Regression models, correlating yield with monthly rainfall and crop growing periods, indicated that the integration of FYM (10 tha⁻¹) with 40 kg N ha⁻¹ was most effective in achieving the highest relative soil quality index (RSQI) of 76 and the greatest sustainability yield index (SYI) of 49.3%. Based on results, we recommend balanced fertilization (N@40 kg ha−1 +10t FYM ha−1) which is easily manageable by farmers as the optimal strategy for improving soil quality and achieving sustainable maize productivity in nutrient depleted Inceptisols of northern India.