The area of vegetable production is growing rapidly world-wide, as are efforts to increase production on existing lands in these labor- and input-intensive systems. Yet information on nutrient losses, greenhouse gas emissions, and input efficiency is lacking. Sustainable intensification of these systems requires knowing how to optimize nutrient and water inputs to improve yields while minimizing negative environmental consequences. This work characterizes soil nitrogen (N) dynamics, nitrate (NO3¯) leaching, greenhouse gas emissions, and crop yield in five diversified vegetable systems spanning a gradient of intensification that is characterized by inputs, tillage and rotational fallow periods. The study systems included a low input organic system (LI), a mechanized, medium scale organic system (CSA), an organic movable high tunnel system (MOV), a conventional system (CONV) and an organic stationary high tunnel system (HT). In a three-year vegetable crop rotation with three systems (LI, HT and CONV), key N loss pathways varied by system; marked N2O and CO2 losses were observed in the LI system and NO3– leaching was greatest in the CONV system. Yield-scaled global warming potential (GWP) was greater in the LI system compared to HT and CONV, driven by greater greenhouse gas flux and lower yields in the LI system. The field data from CONV system were used to calibrate the Root Zone Water Quality Model version 2 (RZWQM2) and HT and LI vegetable systems were used to validate the model. RZWQM2 simulated soil NO3¯-N content reasonably well in crops grown on bare ground and open field (e.g. beet, collard, bean). Despite use of simultaneous heat and water (SHAW) option in RZWQM2 to incorporate the use of plastic mulch, we were not able to successfully simulate NO3¯-N data. The model simulated cumulative N2O emissions from the CONV vegetable system reasonably well, while the model overestimated N2O emissions in HT and LI systems.