The effect of deficit irrigation (DI) on wheat crop yield, soil physical parameters and on nitrate nitrogen movement in soil profile was evaluated under application of dairy manure and nitrogen fertilizer. Two levels of DI were taken as I0.6 (60% FC) and I0.8 (80% FC) along with two dairy manure levels (20 and 25 Mg ha−1) and three nitrogen levels (80, 100, and 120 kg ha−1). The grain yield was high under I0.8 than I0.6, whereas the irrigation level has no significant effect on soil organic carbon contents. Dairy manure, irrigation, and nitrogen indicated strong interaction with each other for all yield-related parameters during both years of study, however, results for 2nd year were highly positive. Soil nitrate nitrogen movement was significantly affected under I0.8 with high rate of dairy manure (25 Mg ha−1) and nitrogen fertilizer (120 kg ha−1). Results concluded that combined application of dairy manure (25 Mg ha−1) and nitrogen fertilizer (120 kg ha−1) under DI level I0.8 resulted in high grain yield. To overcome water scarce conditions, further experiments can be designed by addition of various organic matters in different combination that enhances the yield and soil health.