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Treated wastewater (TWW) infiltration into non-potable aquifers has been used for decades in Western Australia for disposal and reuse. These wastewater treatment plants (WWTPs) are mostly pond systems, infiltrating secondary TWW with some activated sludge. There is no disinfection of TWW pre-infiltration. This study gave an opportunity to study the fate of <i>Escherichia coli</i> (<i>E. coli)</i> in aquifers, using compliance monitoring data (2006&#8722;2016) and is relevant if water reuse is to be implemented at these sites in the future. Microbiological water quality data (<i>E. coli</i>) were evaluated using an advanced statistical method able to incorporate the highly censored data at full scale operational infiltration sites. Subsurface <i>E. coli</i> removal from TWW was observed at all 17 infiltration sites investigated. Most sites (14) had less than six detections of <i>E. coli</i> in groundwater (58&#8722;100% non-detects; 7&#8722;117 samples/bore), thus the statistical method could not be applied. The observations could be used to infer between 1 to &gt;3 log₁₀ removal for <i>E. coli</i>. The remaining three sites had sufficient detections for probabilistic modelling analysis, the median removal efficiency for <i>E. coli</i> was quantified as 96% to greater than 99%, confirming at least 1 log₁₀ removal with potential for several log₁₀ removal. Reductions could not be explained through dilution with the native groundwater alone as there was a high proportion of TWW in observation bores. The observed reductions are likely the result of bacteria retention and inactivation in the aquifer. The magnitude of microbiological water quality improvement highlights the sustainable and reliable use of the aquifer to improve water quality to levels appropriate for low- and medium-risk non-potable uses without using engineered disinfection methods.