Bacteria often respond to dynamic soil environment through the secretion of extracellular polymeric substances (EPS). The EPS modifies cell surface properties and soil pore-scale hydration status, which in turn, influences bacteria transport in soil. However, the effect of soil particle size and EPS-mediated surface properties on bacterial transport in the soil is not well understood. In this study, the simultaneous impacts of EPS and collector size on Escherichia coli (E. coli) transport and deposition in a sand column were investigated. E. coli transport experiments were carried out under steady-state flow in saturated columns packed with quartz sand with different size ranges, including 0.300–0.425 mm (sand-I), 0.212–0.300 mm (sand-II), 0.106–0.150 mm (sand-III) and 0.075–0.106 mm (sand-IV). Bacterial retention increased with decreasing sand collector size, suggesting that straining played an important role in fine-textured media. Both experiment and simulation results showed a clear drop in the retention rate of the bacterial population with the presence of additional EPS (200 mg L−1) (EPS+). The inhibited retention of cells in sand columns under EPS+ scenario was likely attributed to enhanced bacteria hydrophilicity and electrostatic repulsion between cells and sand particles as well as reduced straining. Calculations of the extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) interactions energies revealed that high repulsive energy barrier existed between bacterial cells and sand particles in EPS+ environment, primarily due to high repulsive electrostatic force and Lewis acid-base force, as well as low attractive Lifshitz-van der Waals force, which retarded bacterial population deposition. Steric stabilization of EPS would also prevent the approaching of cells close to the quartz surface and thereby hinder cell attachment. This study was the first to show that EPS reduced bacterial straining in saturated porous media. These findings provide new insight into the functional effects of extrinsic EPS on bacterial transport behavior in the saturated soil environment, e.g., aquifers.