In Belgium, IWVA uses Managed Aquifer Recharge (MAR) to recharge the aquifer with treated wastewater generated from the communities to sustain the potable water supply on the Belgian coast. This MAR facility is faced with a challenge of reduced infiltration rates during the winter season when pond water temperatures near 4 °C. This study involves the identification of the predominant factor influencing the rate of infiltration through the pond bed. Several factors including pumping rates, natural recharge, tidal influences of the North Sea and pond-water temperature were identified as potential causes for variation of the recharge rate. Correlation statistics and linear regression analysis were used to determine the sensitivity of the infiltration rate to the aforementioned factors. Two groundwater flow models were developed in visual MODFLOW to simulate the water movement under the pond bed and to obtain the differences in flux to track the effects of variation of hydraulic conductivity during the two seasons. A 32 % reduction in vertical hydraulic gradient in the top portion of the aquifer was observed in winter causing the recharge rates to fluctuate. Results showed that water temperature caused a 30 % increase in hydraulic conductivity in summer as compared to winter and has the maximum impact on infiltration rate. Cyclic variations in water viscosity, occurring because of seasonal temperature changes, influence the saturated hydraulic conductivity of the pond bed. Results from the models confirm the impact on infiltration rate by temperature influenced hydraulic conductivity.