Nitrogen (N) cycle dynamics and its transport in the ecosystem were always an attracting subject for the researchers. Calculation of N budget in agricultural systems with use of different empirical statistical methods is common practice in OECD and EU countries. However, these methodologies do not include climate and water cycle as part of the process. On the other hand, big scale studies are labor and work intensive. As a solution, various computer modeling approaches have been used to predict N budget and related N parameters. One of them is internationally established Soil and Water Assessment (SWAT) model, which was developed especially for modeling agricultural catchments. The aim of this study was to improve understanding of N leaching with simulation of agricultural land management (fertilization, irrigation, and plant species) in hydrological heavily modified watershed with irrigation-depended agriculture under Mediterranean climate. The study was conducted in Lower Seyhan River Plain Irrigation District (Akarsu) of 9495 ha in Cukurova region of southern Turkey. Intensive and extensive water and nitrogen monitoring data (2008)(2009)(2010)(2011)(2012)(2013)(2014), soil properties, cropping pattern, and crop rotation were used for the SWAT model build, calibration, and validation of the model.