We hypothesized that the transport of Escherichia coli strains harvested from springs could be characterized by a similar set of cell characteristics and transport parameters. The hypothesis was tested by sampling springs throughout the Lubigi catchment in Kampala, Uganda. Chemo‐physical parameters in addition to total coliform concentrations were determined. Furthermore, E. coli strains were harvested, and cell properties determined. Column experiments in saturated quartz columns of 7 cm height were conducted to determine transport parameters of selected E. coli strains. Using a two‐site non‐equilibrium sorption model, transport was modelled by fitting breakthrough data in HYDRUS 1D. Results indicated faecal contamination of the springs with high concentrations of total coliforms, chloride and nitrate. Furthermore, the maximum relative E. coli concentrations (C/C0)max in the column experiments were high. Compared with our previous work on E. coli strains, collected from a pasture and from zoo animals, attachment was low. Modelling revealed that both equilibrium and kinetic sorption were not important under conditions employed in the experiments. These observations are explained by the way in which the strains were harvested: from termination points of flow lines (springs). Such strains may possess characteristics that might have influenced their transport in the subsurface leading to their low attachment efficiency and possibly contributing to the lack of influence of equilibrium and kinetic sorption characteristics. There was no significant correlation between cell properties and transport parameters. Furthermore, 58% of the tested strains were of the O21:H7 serotype, and all definable serotypes identified were associated with diseases. We speculate that this serotype may possess characteristics that allow preferential transport through the aquifers of the area. We demonstrated that bacteria harvested from termination points of flow lines compared with those obtained from pollution sources, which have not undergone transport yet, present a good option for the assessment of bacteria transport characteristics in aquifers. Copyright © 2013 John Wiley & Sons, Ltd.