Abstract: The impact of agricultural practices on soil–groundwater quality in the sub-humid Bekaa plain of Lebanon-East Mediterranean was monitored in four fields (F) between July 2007 and July 2009. These were occupied by continuous mint (F1), summer potato/wheat/potato (F2), lettuce/lettuce/potato/wheat/summer potato (F3) and table grapes (F4). N input calculated on a two-year basis, was in the following ascending order F4, F2, F3 and F1. Soil samples, analyzed down to 200 cm depth, showed high nitrate and chloride concentrations at the end of the 2007 and 2008 seasons. Soil chloride and nitrate peaks recorded in October 2007 and 2008 disappeared below 200 cm overwinter. The calculated N biannual discharge ranged from 130 (F4), to 516 (F2), to 778 (F1), to 879 kg ha−1 (F3). Groundwater quality was studied in 21 wells distributed along a sequence stretching from the Litani River to the eastern water dividing line. Based on the nitrate concentrations, the well located at the top of the water dividing line was the only one suitable for drinking purposes. Eight wells were mildly contaminated, therefore suitable for irrigation purposes except for sensitive crops. Twelve wells, positioned in the plain, showed a nitrate level exceeding 200 mg L−1. Protecting the soil and groundwater quality is a top priority to maintain the ecological and agricultural functions of water.