Concentrations of microbiological contaminants in streams increase during rainfall-induced higher flow ‘event’ periods as compared to ‘baseflow’ conditions. If the stream feeds a drinking water reservoir, such periods of heightened pathogen loads may pose a challenge to the water treatment plant and subsequently a health concern to water consumers downstream. In order to manage this risk, it is desirable to first quantify the differences in surface water quality between baseflow and event conditions. The Event Mean Concentration (EMC) is a flow-weighted average concentration of a contaminant over the duration of a single event, proposed here as a standard parameter for quantifying the net effect of events on microbial water quality. Application of the EMC concept was assessed using flow and quality data for several events from an urbanised catchment. Expected mean EMCs were significantly larger than expected mean baseflow concentrations (p-value≤0.012) for three microbial agents - Escherichia coli (13,000 [n = 7] v. 610 [n = 16] mpn/100 ml), Cryptosporidium (234 [n = 6] v. 51 [n = 16] oocysts/10 litres) and Campylobacter (48 [n = 5] v. 2.1 [n = 16] mpn/100 ml). These parameter estimates were complemented by estimating data variability and uncertainty in the form of second-order random variables. As such the results are in a format appropriate for potential use as components in probabilistic risk assessments evaluating the effect runoff events have on drinking water quality.