The presence of microbial pathogens in surface water run-off from water catchments is a significant problem for many Australian water supply utilities. It is known that the microbial load in surface run-off can increase rapidly during rain events, and then declines a few hours afterwards. For the treatment of such water to ensure drinking water quality to be effective, it is important to have some reliable estimate of the microbial load in the raw water. Real time assessment of microbial load is not possible as accurate laboratory assays are time-consuming and expensive. This paper considers the possible use of alternative, surrogate measures of microbial load derived from physical flow attributes such as volumetric flow rate and turbidity. These measures are relatively easy to obtain and can be monitored automatically to give real-time continuous data streams. We use data collected over the past 2--10 years from a number of Adelaide Hills catchments to calibrate some regression models. A log-log model for microbial load with flow rate as the explanatory variable is shown to be a good fit, but with a sizeable estimated standard deviation. Various possible factors contributing to this variability are discussed. A physical modelling approach is also used to try to understand possible microbial `washout' associated with rain events on a seasonal scale. An improved sampling technique is also suggested, which will potentially assist with obtaining better quality data for use in developing improved regression models in the future.