In this study, simulated solar disinfection of secondary effluent was followed by dark storage at different temperatures or different receiving water matrices. Escherichia coli illumination was followed by 3-day monitoring of the bacterial population and its adaptation in different temperature conditions in the dark. The subsequent survival was linked to the dose received during exposure to light, and results were obtained on the environmentally induced prolongation of survival, maintenance of population or excessive growth, at 4 °C, 20 °C and 37 °C, respectively. An additional set of experiments at 20 °C was subjected to dilution in E. coli-free synthetic wastewater, water from Lake Leman, (synthetic) seawater and Mili-Q water. Post-irradiation monitoring was also conducted, studying 50%, 10% and 1% dilution rates, and the results were attributed to the two parameters of dilution medium and dilution ratio. However, different responses were found based on the acquired dose during pre-treatment. This indicates the importance of the illumination prior to storage, and the preference of bacteria in some matrices over the others. Survival was linked to initial population, dose, dilution and medium; shorter illumination times are to be considered according to the receiving water matrix.