Basin infiltration managed aquifer recharge (MAR) is a commonly used method for storing and treating surface water to be used as drinking water. This study examined how the removal of bacteriophage MS2 was affected by the relative age of the sand used for basin infiltration MAR at 4 °C using batch experiments (static and agitated) and column experiments. The sand and the water used in all experiments were characteristic of that used at a basin infiltration MAR scheme in Uppsala, Sweden. Experimental data was fit with numerical models describing the fate and transport of virus in soil—water systems. The “used” sand that had been subjected to intermittent infiltration over a period of 8 years had 15 times the amount of organic carbon than the “new” sand, which had yet to be used for infiltration. Results showed that attachment of MS2 to the new sand in batch experiments was relatively irreversible. Attachment to the used sand was reversible. Inactivation of MS2 was slowed when it was attached to the used sand. Results for the column experiments showed that the removal rate of MS2 was significantly lower in columns of used sand than in columns of new sand. Simulations indicated that MS2 would be entirely removed in the infiltration basins with new sand. Less than 3 log removals was estimated for basins with used sand. Reduced removal of MS2 by the used sand was deemed to be most likely due to organic coatings on the used sand. Results of this study give deeper insight into the mechanisms responsible for removing virus in infiltration basins and how those mechanisms will change as the sand in the basin is exposed to infiltration water.