Beach sediment and sand are recognized as nonpoint fecal indicator bacteria (FIB) sources capable of causing water quality and health risks for beach-goers. A comprehensive understanding of the key factors and mechanisms governing the migration and exchange of FIB between beach water column and sediment is desired to better predict FIB concentration variations and assess the associated risk. The transport and retention behavior of two model FIB Enterococcus faecalis (E. faecalis) and Escherichia coli (E. coli) was examined using packed-bed columns in both saturated and unsaturated porous media to evaluate FIB migration potentials at conditions simulating the coastal aquatic environment. Additionally, complementary cell characterization techniques were conducted to better understand the migration behaviors of both FIB strains observed in the column experiments. The mobility of the gram-positive species E. faecalis was much more sensitive to solution chemistry and column saturation level than that of the gram-negative species E. coli. Interaction energy calculations suggest that E. faecalis retention was largely governed by the combination of DLVO (Derjaguin-Landau-Verwey-Overbeek) and non-DLVO (most likely hydrophobic and/or polymer bridging) interactions in saturated porous media, while the combination of DLVO and steric interactions controlled the deposition of E. coli cells. The measured surface properties of the two FIB strains supported the distinct bacteria transport behaviors and the differences of the identified mechanisms for each strain. As a result, E. faecalis showed the least affinity to sand in freshwater and appeared to be irreversibly attached in primary energy minima at elevated salt conditions; whereas the retained E. coli cells were reversibly attached and mostly associated with the secondary energy minima at both freshwater and seawater conditions. In unsaturated porous media, E. faecalis cells seemed to prefer to attachment at air/water interface rather than sand surface, while E. coli showed a similar affinity to the two interfaces. It was proposed that the different surface characteristics of the two FIB strains resulted in the distinct transport and retention behavior in porous media. These results highlight the need for FIB management to consider variations in transport behavior between model FIB when assessing water quality and associated risks.