The objective of this research was to study the sorption and transport of bacteriophage MS-2 (a bacterial virus) in saturated sediments under the effect of salinity and soluble organic matter (SOM). One-dimensional column experiments were conducted on washed high-purity silica sand and sandy soil. In sand column tests, increasing salinity showed distinct effect on enhancing MS-2 sorption. However, SOM decreased MS-2 sorption. Using a two-site reversible-irreversible sorption model and the double layer theory, we explained that pore-water salinity potentially compressed the theoretical thickness of double layers of MS-2 and sand, and thus increased sorption on reversible sorption sites. On irreversible sorption sites, increasing salinity reversed charges of some sand particles from negative to positive, and thus converted reversible sorption sites into irreversible sites and enhanced sorption of MS-2. SOM was able to expand the double layer thickness on reversible sites and competed with MS-2 for the same binding place on irreversible sites. In sandy soil column tests, the bonded and dissolved (natural) soil organic matters suppressed the effects of pore-water salinity and added SOM and significantly reduced MS-2 adsorption. This was explained that the bonded soil organic matter occupied a great portion of sorption sites and significantly reduced sorption sites for MS-2. In addition, the dissolved soil organic matter potentially expanded the double layer thickness of MS-2 and sandy soil on reversible sorption sites and competed with MS-2 for the same binding place.