Monitoring of a constructed wetland receiving episodic pulses of subsurface drainage waters from grazed dairy pastures showed good nitrogen reductions, but moderate increases in median Escherichia coli concentrations. This unexpected increase of E. coli was initially postulated to be an artefact of the routine sampling approach, which was biased towards receding flows and likely missed high inflows of contaminated drainage. Intensive monitoring during storm events was therefore instigated using auto-samplers to quantify responses during rainfall-generated flow events. Determination of inflow and outflow E. coli fluxes and loads for ten storm events concluded that the wetland was consistently a net exporter of E. coli with increases ranging from 1.5 to 26-fold (median 10.2-fold). Whilst wildlife defecation in the wetland may account for a proportion of the rise in E. coli, it is likely that (consistent with associated genetic profiling studies) much of the increase is due to mobilisation of environmentally adapted strains of E. coli persisting and growing within the sediment, decomposing plant litter and organic detritus of the wetland. This raises interesting questions regarding the microbial ecology of E. coli and its utility as an indicator of faecal pathogens, and potential health risks from diffuse agricultural drainage after passage through wetlands. Display omitted •Unexpected E. coli increase in a constructed wetland treating agricultural drainage.•In and out-flows, concentrations and loads intensively monitored over 10 stormflows.•Median 10-fold increase in exported E. coli load after passage through wetland.•Credible evidence for persistence and generation of E. coli within the wetland.•Implications for the utility of E. coli as a faecal indicator for human health risk.