In this study, contaminant transport behaviour in the aquifer system (140 m × 180 m × 5 m) was analyzed using a 3-D groundwater flow and contaminant transport model viz. MODFLOW2005 and MT3DMS. The impacts of hydrodynamic dispersion parameters on the conservative contaminant plume dynamics were analyzed for homogeneous and heterogeneous aquifer systems with low permeability porous media (LPPM). The spatio-temporal distribution of contaminant concentration and breakthrough curves (BTCs) at 12 observation wells were used to analyze the transport dynamics due to conservative contaminant released from a single point source over a hypothetical study area for a period of 1 year (365 days). Results from MODPATH show a significant variation in the pathway of groundwater for homogeneous and heterogeneous aquifer systems. During the source loading period, a very low value of concentration of order 10-9 mg/m3 was observed in the LPPM region. The spatial distribution of contaminant plume for aquifer system with LPPM varied largely as compared to homogeneous aquifer system. The maximum value of concentration in the aquifer with LPPM was found to be ~40% higher than the homogeneous system after source removal. After the source removal, the maximum value of 1.98 mg/m3 was observed for the homogeneous system at a location away from pumping and extraction well after 730 days; however, for a heterogeneous system with LPPM, the maximum value of 2.57 mg/m3 was observed. An early breakthrough was observed for αL= 54 m as compared to αL= 9 m for homogeneous aquifer system, clearly depicting the effect of longitudinal dispersivity on BTC. However, effects of dispersivity on the rising and falling limbs of the BTC were negligible for heterogeneous aquifer system with LPPM. Further, an impact of LPPM and longitudinal dispersivity on the peak concentration value at observation well (OBS-7) was undistinguishable. The numerical simulations carried out in this study mimic the realistic heterogeneous aquifer conditions and highlighted the relevance of LPPM and associated transport processes on contaminant transport dynamics at field-scale, which was usually overlooked.