In the last decade, flooding has caused the death of over 60,000 people and affected over 900 million people globally. This is expected to increase as a result of climate change, increased populations and urbanisation. Floods can cause infections due to the release of water-borne pathogenic microorganisms from surcharged combined sewers and other sources of fecal contamination. This research contributes to a better understanding of how the occurrence of water-borne pathogens in contaminated shallow water bodies is affected by different environmental conditions. The inactivation of fecal indicator bacteria Escherichia coli was studied in an open stirred reactor, under controlled exposure to simulated sunlight, mimicking the effect of different latitudes and seasons, and different concentrations of total suspended solids (TSS) corresponding to different levels of dilution and runoff. While attachment of bacteria on the solid particles did not take place, the decay rate coefficient, k (d⁻¹), was found to depend on light intensity, I (W m⁻²), and duration of exposure to sunlight, T (h d⁻¹), in a linear way (k = k_D+ 0.03·I and k = k_D+ 0.65·T, respectively) and on the concentration of TSS (mg L⁻¹), in an inversely proportional exponential way (k = k_D+ 14.57·e^{−0.02·[TSS]}). The first-order inactivation rate coefficient in dark conditions, k_D= 0.37 d⁻¹, represents the effect of stresses other than light. This study suggests that given the sunlight conditions during an urban flood, and the concentration of indicator organisms and TSS, the above equations can give an estimate of the fate of selected pathogens, allowing rapid implementation of appropriate measures to mitigate public health risks.