A study was undertaken to determine the potential inactivation rates of selected enteric microorganisms in captured urban stormwater within a constructed reedbed and in tertiary carbonated aquifer during an Aquifer Storage, Transfer and Recovery (ASTR) scheme. The study was undertaken in-situ in the constructed reedbed and aquifer using diffusion chambers. The results showed that all tested bacteria had one log(10) reduction time of less than 6 and 2.5 days respectively in constructed reedbeds and aquifer, which suggests that presence of enteric bacteria in the recovered water is unlikely. However, adenovirus and Cryptosporidium oocysts showed lower inactivation rates with one log(10) reduction times of more than 33 days in the constructed reedbeds. This means that the constructed reedbed with a mean residence time 10 days cannot be relied upon as an efficient treatment barrier for virus and protozoa. Storage of stormwater in aquifer with brackish water resulted in slow inactivation of enteric viruses over the 35 day incubation period with adenovirus and rotavirus showing slowest inactivation times (extrapolated T(90) of >100 days). Cryptosporidium oocysts showed similar inactivation rate in the constructed reedbed and aquifer.