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Aquifer microbial water quality evaluations are often performed by collecting groundwater samples from monitoring wells. While samples collected from continuously pumped sources are seldom disputed as representative of the aquifer, natural biofilm present in the vicinity of well screens may introduce unwanted microbial artefacts in monitoring wells that are only periodically sampled. The need for well water purging to obtain samples void of these artefacts has been widely recognized. However, purging methods are not standardized; many approaches presume that physico-chemical water quality stability achieved through the removal of 3 to 5 well volumes is indicative of the stability of target analytes. Using a data set collected from a shallow unconfined aquifer in Southern Ontario, Canada, the need for using dedicated approaches that account for the time-dependent nature of microbial water quality changes was demonstrated. Specifically, the utility of adenosine triphosphate (ATP) as a rapid, field-ready biochemical indicator of microbial water quality stability was investigated. This work shows that ATP concentrations reflect time-limited (bio)colloid transport processes that are consistent with other microbial water quality parameters monitored, but different from commonly measured physical and chemical water quality indicators of well purging adequacy. ATP concentrations occasionally fluctuated even after 3 or 4 h of purging, indicating that microbial artefacts attributable to biofilms in the vicinity of the well screen can still persist. The recurrence of characteristic ATP patterns in each well was systematically examined through the novel application of dynamic time warping (DTW), a nonparametric time series analysis approach. These patterns are believed to be linked with seasonal hydrogeological conditions, which warrant consideration in the design and interpretation of subsurface microbial water quality investigations.