Managed aquifer recharge and changes in crop type or nutrient management on agricultural lands are promising approaches to address groundwater quality degradation by nitrate. Tools to assess nonpoint-source contaminant transport are needed to better understand the interaction between agricultural management practices and long-term nitrate dynamics in groundwater basins. This study investigates the impact of time-resolution upscaling of groundwater flow stresses (i.e., recharge, pumping, and evapotranspiration rates) on the long-term prediction of nitrate transport at the regional scale. A three-dimensional, monthly transient flow and nitrate-transport model using MODFLOW and MT3D is applied as the reference simulation. The reference model results are compared to temporally upscaled models with (1) upscaled annual-averaged flow and transport stresses and (2) steady-state flow stresses, across different management scenarios. Models with annual-averaged flow and nitrate-loading stresses were found to be the best alternative to the reference model. However, employing a steady-state flow field to parameterize transient transport models, using a time series of spatially variable annual total contaminant loading, provides a useful alternative to predict the trend and variability of nitrate-concentration breakthrough curves at wells across the regional scale and to differentiate the effects of various agricultural management scenarios, if the history of the source contaminant mass is known. The difference between concentrations resulting from steady-state-flow versus transient-flow models is less than 2 mgN/L for nearly 75% of shallow groundwater cells in the model. However, the steady-state-flow-model-based transport simulation does not capture short-term oscillations of nitrate concentrations in pumping wells at the local scale.