Column experiments were conducted to investigate the transport and deposition behavior of representative hydrophobic and hydrophilic bacteria strains in sand at different water saturations. These strains are similar in surface charge, shape, and size, and differ primarily in their surface hydrophobicity and tendency to form aggregates. The amount of bacteria that were retained in the sand increased with decreasing water saturation, especially for the more hydrophobic strain that formed larger cell aggregates. Most of the cells were retained close to the column inlet, and the rate of deposition rapidly decreased with depth. The experimental data were analyzed using a mathematical model that accounted for deposition on two kinetic sites. Consideration of depth-dependent deposition in the model formulation significantly improved the description of the data, and the amount of cell retention was typically dominated by this site. The depth-dependent deposition coefficient tended to increase with decreasing water content, especially for the hydrophobic bacteria. Straining is believed to account for these observations because it increases in magnitude with increasing cell and aggregate size and when a greater fraction of the water flows through a larger number of small pore spaces with decreasing water content. Cell retention on the other kinetic deposition site was well described using a conventional model for attachment and detachment. Consistent with interaction energy calculations for bacteria attachment, however, low amounts of cell retention occurred on this site. Attempts to separately determine the amounts of attachment to solid–water and air–water interfaces were confounded by the influence of straining.