Over and ill-timed application of nitrogen (N), intensive tillage and heavy irrigation could lead to build up of residual nitrate in surface as well as subsurface soil layers, low fertilizer use efficiency and contamination of ground and surface water with nitrates. This is particularly true in wheat-maize crop rotation where high rates both of N and irrigation and intensive tillage are practiced to get higher yields. However, limited literature is available on the fate of applied N in wheat–maize cropping system in response to tillage, irrigation and fertilizer practices in Pakistan. Hence two experiments were conducted in the Research Area, Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad to assess the effect of irrigation, nitrogen and fertilizer practices on soil properties, crop yield, carbon sequestration and NO3-N under wheat-maize cropping sequence for two consecutive years from 2011-2013. In the first study, treatments comprised of three levels of irrigation and four levels of N in split plot design. Three levels of irrigation were 0.7, 1.0 and 1.3 of the estimated evapo-transpiration (ETc). The four N levels were 0, 110, 160 and 210 kg N ha-1 for wheat and 0, 200, 250 and 300 kg N ha-1 for maize, the recommended rate N for wheat (Triticum aestivum L.) and maize (Zea mays L) in this area is 110 and 200 kg ha-1, respectively. The N was applied either in two splits (50% at sowing + 50% at maximum tillering for wheat, 50% at sowing + 50% at knee height for maize) or three splits (50% at sowing + 25% at maximum tillering + 25% at spike initiation for wheat, 50% at sowing + 25% at knee height + 25% at tasseling for maize), therefore making a total of seven N treatments. In the second experiment, same cropping system was followed, however recommended rate of N (110 and 200 kg N ha-1 for wheat and maize, respectively) was sourced from either urea or combination of urea and farm manure (FM). Thus, there were three fertilizer treatments F1 (100% N from urea), F2 (75% N from urea and 25% N from FM) and F3 (50% N from urea and 50% from FM) at three tillage systems namely MT (minimum tillage), CT (conventional tillage) and DT (deep tillage). The treatments were replicated three times in split plot design using tillage in main plots and fertilizer practices in sub plots. The data on growth and yield parameters were recorded for both the crops at harvest. Before sowing the first crop and after harvesting fourth crop, soil samples were collected and characterized for physical (bulk density, soil saturated hydraulic xx conductivity and total porosity) and chemical (soil organic carbon and nitrate-N) properties following standard procedures. The results from the first study indicated that N at 110 and 250 kg ha-1 for wheat and maize crops, respectively not only increased growth, yield and water use efficiency of both the crops during both the years but also decreased buildup of NO3-N in soil. Application of N in 3 unequal splits (50%+25%+25%) proved better than application of N in 2 equal splits (50%+50%) in terms of improved crop yield, crop N recovery, water use efficiency and less accumulation of NO3-N in soil profile. Application of irrigation water according to crop water requirement was the best treatment in terms of better yield, crop N recovery and water use efficiency along with lower leaching of NO3-N into sub-soil. Deficit irrigation resulted in lower crop yield and higher buildup of residual NO3-N in soil. In contrast, excessive irrigation did not have any additional benefits in terms of crop yield, however resulted in lower water use efficiency and crop N recovery and greater concentration NO3-N in lower depths of soil. Results from the second field study revealed that deep tillage and conventional tillage along with combined application of inorganic and organic N sources (half N from urea + half N from FM) resulted in lower bulk density, higher saturated hydraulic conductivity and root length density (RLD) compared that with the minimum tillage. The results indicated that MT resulted in significantly higher SOC pools in surface soil (0-10 cm), conversely DT and CT caused high SOC pools in 10-40 cm soil depths. Therefore, averaged across 0-40 cm, DT and CT proved better in terms of SOC pools. The DT and CT caused greater RLD and stocks of total N and available P in soil with DT and CT compared to that with MT caused significantly higher crop yield. The DT and CT also resulted in significantly greater accumulation of NO3-N in soil compared to that with MT treatment.