- Abstract Escherichia coli is the leading indicator of microbial contamination of natural waters, and so its in-stream fate and transport needs to be understood to eventually minimize surface water contamination by microorganisms. To better understand mechanisms of E. coli release and transport from soil sediment in a creek the artificial high-water flow events were created by releasing 60–80 m 3 of city water on a tarp-covered stream bank in four equal allotments in July 2008, 2009 and 2010. A conservative tracer difluorobenzoic acid (DFBA) was added to the released water in 2009 and 2010. Water flow rate, E. coli and DFBA concentrations as well as water turbidity were monitored with automated samplers at three in-stream weirs. A one-dimensional model was applied to simulate water flow, and E. coli and DFBA transport during these experiments. The Saint–Venant equations were used to calculate water depth and discharge while a stream solute transport model accounted for release of bacteria by shear stress from bottom sediments, advection-dispersion, and exchange with transient storage (TS). Reach-specific model parameters were estimated by evaluating observed time series of flow rates and concentrations of DFBA and E. coli at all three weir stations. Observed DFBA and E. coli breakthrough curves (BTC) exhibited long tails after the water pulse and tracer peaks had passed indicating that transient storage (TS) might be an important element of the in-stream transport process. Comparison of simulated and measured E. coli concentrations indicated that significant release of E. coli continued when water flow returned to the base level after the water pulse passed and bottom shear stress was small. The mechanism of bacteria continuing release from sediment could be the erosive boundary layer exchange enhanced by changes in biofilm properties by erosion and sloughing detachment.