Unsaturated zone N fate and transport were evaluated at four sites to identify the predominant pathways of N cycling: an almond [Prunus dulcis (Mill.) D.A. Webb] orchard and cornfield (Zea mays L.) in the lower Merced River study basin, California; and corn–soybean [Glycine max (L.) Merr.] rotations in study basins at Maple Creek, Nebraska, and at Morgan Creek, Maryland. We used inverse modeling with a new version of the Root Zone Water Quality Model (RZWQM2) to estimate soil hydraulic and nitrogen transformation parameters throughout the unsaturated zone; previous versions were limited to 3-m depth and relied on manual calibration. The overall goal of the modeling was to derive unsaturated zone N mass balances for the four sites. RZWQM2 showed promise for deeper simulation profiles. Relative root mean square error (RRMSE) values for predicted and observed nitrate concentrations in lysimeters were 0.40 and 0.52 for California (6.5 m depth) and Nebraska (10 m), respectively, and index of agreement (d) values were 0.60 and 0.71 (d varies between 0 and 1, with higher values indicating better agreement). For the shallow simulation profile (1 m) in Maryland, RRMSE and d for nitrate were 0.22 and 0.86, respectively. Except for Nebraska, predictions of average nitrate concentration at the bottom of the simulation profile agreed reasonably well with measured concentrations in monitoring wells. The largest additions of N were predicted to come from inorganic fertilizer (153–195 kg N ha⁻¹ yr⁻¹ in California) and N fixation (99 and 131 kg N ha⁻¹ yr⁻¹ in Maryland and Nebraska, respectively). Predicted N losses occurred primarily through plant uptake (144–237 kg N ha⁻¹ yr⁻¹) and deep seepage out of the profile (56–102 kg N ha⁻¹ yr⁻¹). Large reservoirs of organic N (up to 17,500 kg N ha⁻¹ m⁻¹ at Nebraska) were predicted to reside in the unsaturated zone, which has implications for potential future transfer of nitrate to groundwater.