Agricultural contamination of groundwater in northwestern Mississippi, USA, has not been studied extensively, and subsurface fluxes of agricultural chemicals have been presumed minimal. To determine the factors controlling transport of nitrate-N into the Mississippi River Valley alluvial aquifer, a study was conducted from 2006 to 2008 to estimate fluxes of water and solutes for a site in the Bogue Phalia basin (1,250 km2). Water-quality data were collected from a shallow water-table well, a vertical profile of temporary sampling points, and a nearby irrigation well. Nitrate was detected within 4.4 m of the water table but was absent in deeper waters with evidence of reducing conditions and denitrification. Recharge estimates from 6.2 to 10.9 cm/year were quantified using water-table fluctuations, a Cl- tracer method, and atmospheric age-tracers. A mathematical advection-reaction model predicted similar recharge to the aquifer, and also predicted that 15% of applied nitrogen is leached into the saturated zone. With current denitrification and application rates, the nitrate-N front is expected to remain in shallow groundwater, less than 6–9 m deep. Increasing application rates resulting from intensifying agricultural demands may advance the nitrate-N front to 16–23 m, within the zone of groundwater pumping.