Agricultural production being an integrated interactive effect of soil-water-fertilizer-climate continuum, a judicious and scientific management of this complex system is crucial for enhancing crop productivity on a sustained basis. Among the various inputs, water and fertilizer (nutrients) are considered as the two key inputs making maximum contribution to crop productivity. Soil management through tillage can further optimize their use efficiencies. A long term experiment was initiated in 2001 to quantify the integrated plant nutrient-water-tillage interactions in Rice-Wheat and Maize-Wheat cropping systems. The treatments consisted of two tillage, three water regimes and twelve nutrient levels. The nutrient treatments were: Control (No nitrogen), 75% NPK (75 represents 75 per cent of the recommended dose for nitrogen), 100% NPK, 150% NPK, 75% NPKF (25% N substituted by FYM), 100% NPKF (25% N substituted by FYM), 150% NPKF (25% N substituted by FYM), 100% NPK + Green manure (Sesbania), 100% NPKB (25% N substituted by Bio-fertilizers), 100% NPKS (25% N substituted by Sewage Sludge), 100% NPK + crop residues incorporated (of the previous crop), and Fully Organic (50%FYM, 25% Bio-fertilizer, 25% Sewage Sludge). In rice, the tillage treatments were puddled (transplanted) and dry seeded (non-puddled) while in maize it was bed planting and conventional flat-bed planting. In wheat, it was conventional tillage and no-tillage treatments. The water regimes were unlimited water availability (continuous submergence in rice, three irrigations in maize and five irrigations in wheat), adequate water availability (one day drainage in rice, two irrigations in maize and three irrigations in wheat) and limited water availability (three day drainage in rice, one irrigation in maize and three irrigations in wheat). The experiment was initiated by growing Rice in Rice-Wheat cropping systems and Maize in Maize-Wheat cropping systems during the monsoon (kharif) season followed by wheat in the winter (rabi) season. Detailed observations on various aspects such as soil physical and chemical parameters, major and micronutrients and microbiological aspects of the experiment were being monitored periodically. The results have indicated that there are significant interactions between tillage, water regimes and nutrient levels in both the cropping systems. The effect of puddled and non-puddled conditions in rice also influenced the water and nutrient uptake. Organic carbon and microbial biomass carbon exhibited increase in the plots receiving application of organic manures (particularly FYM), green manure and biofertilizers in conjunction with inorganic fertilizers. Compared to non-puddled conditions, puddling was associated with increase in organic carbon content whereas microbial biomass carbon was higher in the non-puddled paddy plots. Under continuous submerged conditions, organic carbon appreciated whereas reduction was conspicuous in the microbial biomass carbon conditions. In rice, the yield of transplanted crop was better than the dry seeded treatment while the water regimes treatment of irrigating one day after disappearance of water had a positive impact on soil quality. In Maize-Wheat cropping system, it was conclusively established that tillage-water-nutrient interactions have significantly affected the soil physical quality. Nutrient management significantly increased the organic carbon content in soil, macro- and micro- aggregates under both the cropping systems. Under both the cropping systems, effect was more pronounced in the plots receiving 100% organics, followed by green manure and FYM-treated plots. Build-up of organic carbon was relatively higher in macro-aggregates compared to soil and micro-aggregates. No-tillage applied to wheat positively influenced the organic carbon content in soil, macro- and micro-aggregates. The treatments receiving whole amount of N through inorganic source recorded maximum NH4-N at all the depths, while partial or full substitution of fertilizer with organics substantially reduced the downward translocation of NH4-N. In case of the water regimes, the wettest water regime (unlimited water availability) treatment maintained highest NH4-N levels throughout the profile, followed by the adequate water availability treatment and limited water avaialability under both the cropping systems. Under both the cropping systems, in the surface soil and aggregates, NO3-N was more under the plots treated with 100% N + green manure (GM) followed by 100% N + crop residues. The highest NO3-N content in the soil, macro- and micro-aggregates in the surface layer was found under minimum water regimes under both the cropping systems, while NO3-N content was highest in the unpuddled soil in the rice-wheat and in bed planted soil of maize-wheat system. Application of N through organics or integrated sources showed relatively higher amount of available P under both the cropping systems. Puddling in rice maintained a higher amount of available P as compared to unpuddled soils, whereas conventionally-tilled soil contained higher amount of available P compared to that under bed-planted soil under maize-wheat. Higher available P content was associated with maximum water regimes followed by optimal and sub-optimal water regimes under both the systems. In general, Organic Carbon (OC) and labile fraction-C values were relatively more in rice-wheat than maize-wheat system. A model called CropSyst was calibrated and validated for the maize-wheat cropping system.