AbstractDuring the evolution of meander bends, the intra‐meander groundwater head gradients steepen and generate zones of accelerated water and nutrient intra‐meander fluxes important for ecosystem processes. This paper compares and contrasts three MODFLOW groundwater model packages based on their simulation of intra‐meander flux for two stages of meander evolution observed in a sandbox river table and one level of river bed clogging, where the hydraulic conductivity in the river bed is lower than in the adjacent aquifer. These packages are the Time‐Variant Specified Head package [constant head (CHD)], River package (RIV), and Streamflow‐Routing package (SFR2), each controlling the groundwater or river head bounding the intra‐meander region. The RIV and SFR2 packages fix river stage and allow for variation in groundwater head below the river, which is suggested for simulating intra‐meander flux for all sinuosities with and without river bed clogging whenever river bed parameters are available. The CHD package fixes below river groundwater head and fails to simulate intra‐meander head loss and flux in meanders with high sinuosity or river bed clogging. In low sinuosity meanders and in cases without river bed clogging, there were no significant differences between MODFLOW packages for simulating river intra‐meander head loss and flux. This research demonstrates why MODFLOW users need to consider the limitations of each package when simulating intra‐meander flux in reaches with river bed clogging, high sinuosity, or similarly steep hydraulic gradients. Copyright © 2014 John Wiley & Sons, Ltd.