In Pakistan, there are many factors contributing to the average low yield of wheat, maize and many other crops. Irrigation scheduling to field crops is still disregard to soil specific water requirement of crops and basic principles of sustainability and resource conservation. On the other hand, the fertility of agricultural soils in Pakistan is too low inherently to support crop production. However, the intensive agriculture through irrigation, fertilizer and other management practices aimed at increasing crop yields has introduced an enduring threat of groundwater pollution by unused N fertilizer and pesticide leaching from the irrigated fields. One Lysimeter and two field trials were conducted for two years with wheat-fallow-maize rotation at the research farm (latitude, 31°-26'' N and 73°-06'' E; altitude, 184.4 m), Institute of Soil and Environmental Sciences, University of Agriculture Faisalabad, Pakistan, to access the effect of irrigation, nitrogen and manure rates on pesticides and NO 3- movement, soil properties, and yield of wheat and maize. A Lysimeters trial was conducted using two manure levels (0 and 50 Mg ha -1 ) along with a basal dose of NPK and two irrigation levels (32.5 and 47.5 cm) applied to wheat crop, while hybrid maize was grown with residual effect of manure in addition to the basal dose of NPK using two irrigation levels (45 and 60 cm). Field Trial-1 was also conducted with similar treatments but with split plot arrangement keeping manure in the main plots and irrigation levels in subplots. The second field trial was conducted in a wheat-fallow-maize rotation with three irrigation levels (32.5, 40.0 cm and 47.5 cm for wheat, and 37.5, 52.5 and 67.5 cm for maize crop) and three N levels (100, 130 and 160 kg ha –1 to wheat crop, and 220, 270 and 320 kg ha –1 ). Ceramic cups/solution samplers already installed at 35, 70, 115 and 160 cm depths in each lysimeter were used for leachates collection while under field conditions ceramic cups were installed at 35, 70 and 110 cm depth. To access the nitrate leaching at 115 cm and 110 cm from the lysimeter and field trials, respectively, drainage was measured by water balance equation, where ET c was calculated by encountering stress factor and crop coefficient to Penman Montieth-FAO56 equation. A Model “Hydrus-1D” was used to predict the ET c and drainage, where it was calibrated using the data of water balance at 115 cm depth for lysimeters and 110 cm for both field trials of year-1 and validated to simulate the drainage during year-2. Soil water retention curve and soil hydraulic parameters were measured using RETC-fit model, while other soil physicochemical properties were measured according to standard methods. Isoproturon and xviiiAtrazine were applied to wheat and maize after 1 st irrigation and soil samples were collected from different soil depths for their residues after 280 and 65 days after application (DAA), respectively. Soil samples from 0-35 (with and with out manure), 35-70 and 70-110 cm from field tiral-1 were colleted for Isoproturon and Atrazine sorption study. Sorption results indicated that Isoproturon and Atrazine K d linearly correlated with the amount of organic carbon in the soil (SOC). The organic carbon partition coefficients (K oc ) of Isoproturon and Atrazine averaged 240.1 and 184.9 L kg -1 , respectively and remained almost constant for different SOC levels representing different soil layers, however a higher K oc was observed at low spiking solutions indicating the concentration dependent behaviour of sorption. Isoproturon residues 280 DAA with two manure and two irrigation levels ranged 2.10-3.59% under lysimeter and 1.54-3.13% under field conditions, however Atrazine residues under respective trials 65 DAA ranged only 0.62- 0.78% and 0.88-2.82%, where lowest residues were observed with frequent irrigation applied to manure amended soil. Ground water ubiquity score (GUS) indicated that in the absence of manure under both irrigation levels, Isoproturon touched the critical limit of 1.8 to be considered as leacher, while with the application of manure it could be considered as non leacher. Atrazine GUS ranged from 1.7- 1.9, indicating it as non leacher. Manure application at 50 Mg ha -1 along with the basal dose of NPK was cost effective which not only increased the yield of wheat by 35 and 40 % under lysimeters and field condition, respectively, but its residual effect was also effective in increasing the grain yield of the respective maize trials by 14 and 26 %. The improved soil physical properties, i.e. higher infiltration rate and hydraulic conductivity, and decreased bulk density were additional advantages of manure. Manure also increased the available water capacity and SOC contents of the soil. Heavy irrigation although boosted up the yield of wheat and maize crop, however due to improper irrigation scheduling it increased the drainage and ultimately the nitrate leaching to a lower depth. Long fallow rainy season showed heavy drainage, i.e. 9-13 cm at 115 cm depth and 8-14 cm at 110 cm depth under lysimeter and field condition, respectively, which ultimately increased the NO 3- leaching in respective trials by 2.4-3.2 kg ha -1 and 4.6-6.0 kg ha -1 which was especially high in the manure receiving plots, where its concentration increased the critical limit of safe drinking water. Our results indicated that critical readily available water was 16.5 to 18.5 % for wheat and 16 to 20 % for maize crop, which was lowest at minimum temperature and vice versa.