This study was conducted to assess the nutrients losses from parts representative of Mardan and Charsadda soils through subsurface tile drainage system installed under Salinity Control and Reclamation Project (SCARP). The subsurface drainage system was executed during 1979-1992 whereby 150 m long lateral porous pipes were installed at a depth to 2.0 to 3.0 m with 90 m spacing. The lateral pipes were connected to a 1200 m long main collector pipe opening into main open drain. To achieve this objective, samples of irrigation waters, drainage waters and soils samples (to a depth of 270 cm with 45 cm increment from surface) were periodically collected for three cropping seasons during 2003-05. Drainage water samples were collected for the post irrigation timings of 24, 30, 36, 48, 72 and 96 h for each irrigation applied to the two sites, Fazliabad, Mardan and Manga Dargai Charsadda selected on the basis of a field survey of the area. Samples of irrigation waters (iw), drainage water (dw) and soils were analyzed for pH, EC, Na, Ca, Mg, SAR, N, P, K, Cu, Fe, Mn and Zn. The total input and removal of salts and nutrients were estimated using the concentration of a nutrient multiplied by volume of water and yield of a crop in a given season. The field survey indicated that after SCARP execution the cropping intensity and crop yields increased three to four fold. Poplar (Populus alba) plantation disturbed the tiles and resulted in blockage and breakage of drainage pipes in parts of the area. The banks of irrigation waters revealed the soil erosion and subsidence to weak matrix associated with leaching of Ca and Mg. Nutrients requirements have gone up and need to be supplied proportionately to get higher yield of the crops. The values of pH and EC of irrigation water showed limited variation with time and seasons. The pHiw and ECiw of site-2 applied were higher compared to site-1.The values of EC, Ca, Mg, Na and SAR were in the range permissible for irrigation in both sites. Mean seasonal values of pH, EC, [Ca] and [Mg] were higher for irrigation waters applied to maize during 2004 as compared to water applied during 2003-04 and 2004-05 applied to wheat crop, while [Na] in both successive seasons of 2004 and 2004-05 were lower than the mean values recorded for the season 2003-04. Although the values of NH4-N, NO3-N, P, and K and micronutrients in irrigation waters appeared low but their total input over the cropping season in six irrigations may be important for crop growth. For instance the seasonal addition of readily bio- available NH4-N, NO3-N, P and K ranged between 1.24 to 3.36, 1.85 to 4.24, 0.56 to 2.88 and 6.86 to 12.3 kg ha-1, respectively in irrigation water. Statistical analysis using factorial model (sampling time x 6 locations over time x 2 replications over locations x 6 sampling depth) revealed that all these factors significantly (P<0.001) influenced soil pH, EC, Na, Ca, Mg, SAR, organic matter, NH4-N,(except location/time), NO3-N, (except sampling time and location over time), P (except replication/location), K, Cu, Fe, Mn and Zn (except replication/location). Soils were silt loam, alkaline, strongly calcarious non saline, low in organic matter, low in Ca, Mg in relation to Na, low in N, P and adequate in K. Soils were permeable and that the leaching fraction determined in disturbed surface soil (0-45 cm) samples varied between 0.1 to 0.28 in site-1 and 0.16 to 0.24 in site-2 during 1st year. Leaching of salts and migration of clay was suggested by increasing levels to lower depths. The concentrations of nutrients showed significant variations with depth, time and sites. Based on statistical factorial analysis [2 sites x 3 seasons x 6 irrigation x 6 post irrigations sampling timing], sites, cropping season and number of irrigation induced significant variations in the values of pH, EC, Ca, NH4-N, P, and K concentrations in drainage waters, collected after each irrigation at the given timings. Sites showed non- significant difference in Mg, NO3-N while P varied non-significantly with number of irrigation and Mg with cropping season. The post irrigation sampling had significant effect on [Na]dw only. The [Cu]dw and [Zn]dw varied significantly (p < 0.05) only with seasons while [Mn]dw showed significant (p < 0.05) differences in sites and seasons. When averaged across other factors, site-2 maintained higher mean values of pH, EC, Ca, NH4-N, P, Fe, and lower values of K while concentrations of Mg, NO3, Cu and Mn were statistically similar in both sites. Higher values of these ions in site-2 could be associated with its higher concentrations in irrigation water which had its source from a large drain collecting canal seepage while stie-1 was irrigated directly with canal waters. When averaged across other factors, mean values of EC, Na, NO3 and Fe were higher in drainage waters collected during 2003-04, pH, Ca, Mg and Mn were higher during 2004 and those of NH4, P, K and Zn were higher in 2004-05 than other years, respectively. The mean values of [Na]dw were several folds greater than [Ca]dw and [Mg]dw. [NO3- N]dw were 2.5 times greater than [NH4-N] and [P]dw which were four to ten times lower than K. Similarly mean values of [Cu]dw were four times greater than [Zn]dw. This trend was consisted with concentrations observed in irrigation water, notwithstanding the variations from year to year and site to site. All these nutrients concentrations were invariably higher in dw than iw. The observed seasonal losses with drainage waters ranged from 1.6 to 8.2 (NH4-N), 0.7 to 22.9 (NO3-N), 0.32 to 7.0 (P), 18.5 to 53.4 (K) in site-1 and 1.2 to 7.5, 1.2 to 13.7, 1.4 to 6.5 and 14.9 to 35.5 kg ha-1 for the given nutrients in site-2, respectively in 2003-04. More or less similar losses were observed with some variations in the subsequent years. Nutrient balance suggested the losses through drainage and removal by crops generated negative balance in fields where no or lower doses of N, P and K were added. It is concluded that adequate fertilizers addition is imperative for maintaining soil fertility and to obtain optimum yields under the given irrigation-crop- drainage system.