High concentration ammonium (NH4+) discharges from aerated lagoon effluent (ALE) correlated to eutrophication of receiving waters. This study presents the first attempt to scrutinise the mass transfer mechanism of NH4+ from ALE onto the granular activated carbon (GAC) in batch and plug-flow column (PFC) studies. The GAC was characterised by BET surface, X-ray fluorescence, scanning electron microscopy, X-ray diffraction and Fourier transform infrared spectroscopy. The kinetics and isotherm models were applied to experimental data to understand adsorption behaviour, while mass transfer factor (MTF) models was used to determine global, external, and internal mass transfer. The PFC was successfully applied for the removal of NH4+ from ALE. The results showed that the adsorption of NH4+ from ALE on the GAC followed the pseudo-second-order kinetic model and the Freundlich adsorption isotherm in batch study. The resistances of mass transfer for adsorption of NH4+ onto GAC from the PFC are verified. The use of these empirical models has been proved that the models were very suitable for PFC design and understanding mechanism of mass transfer of solutes from waters onto porous materials.