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Bacterial contamination of groundwater has always been an ecological problem worthy of attention. In this study, <i>Salmonella enterica</i> serovar Typhimurium with different flagellar phenotypes mainly characterized during host-pathogen interaction were analyzed for their transport and deposition behavior in porous media. Column transport experiments and a modified mobile-immobile model were applicated on different strains with flagellar motility (wild-type) or without motility (Δ<i>motAB</i>), without flagella (Δ<i>flgKL</i>), methylated and unmethylated flagellin (Δ<i>fliB</i>), and different flagella phases (<i>fliC^ON</i>, <i>fljB^ON</i>). Results showed that flagella motility could promote bacterial transport and deposition due to their biological advantages of moving and attaching to surfaces. We also found that the presence of non-motile flagella improved bacterial adhesion according to a higher retention rate of the Δ<i>motAB</i> strain compared to the Δ<i>flgKL</i> strain. This indicated that bacteria flagella and motility both had promoting effects on bacterial deposition in sandy porous media. Flagella phases influenced the bacterial movement; the <i>fliC^ON</i> strain went faster through the column than the <i>fljB^ON</i> strain. Moreover, flagella methylation was found to favor bacterial transport and deposition. Overall, flagellar modifications affect <i>Salmonella enterica</i> serovar Typhimurium transport and deposition behavior in different ways in environmental conditions.