In certain countries where fresh water is in short supply, the effluents from wastewater treatment plants are being recycled for other uses. For quality assurance, tertiary disinfection treatments are required. This study aims to evaluate the inactivating efficacy with an ultraviolet (UV) system on fecal bacteria from effluents of urban wastewater treatment facilities and the post-treatment influence of the environmental illumination. The effect from different UV doses was determined for native and standardized lyophilized strains of Escherichia coli right after the irradiation as well as after 24 h of incubation under light or dark conditions. To achieve 3 log-reductions of the initial bacterial concentration, a UV dose of approximately 12 mJ cm−2 is needed for E. coli ATCC 8739 and native E. coli. However, there is a risk of the reactivation of 0.19% and 1.54% of the inactivated organisms, respectively, if the treated organisms are stored in an illuminated environment. This suggests that the post-treatment circumstances affect the treatment success; storing the treated water under an illuminated environment may pose a risk even if an effective inactivation was achieved during the irradiation.