water that minimises the risk of infection to downstream consumers. The nature of the contamination and the mechanisms that control contaminant dynamics may vary considerably due to either site-specific or contaminant-specific properties and hence there is a need to better understand how to assess and mitigate the risks. As indicated above, microbial contaminants such as the (oo)cysts of the pathogens Crytposporidium or Giardia, are mainly derived from allochthonous (external) sources, whereas others may be generated autochthonously (internally) within the water storage. It is therefore not surprising that a fundamental principle of drinking water supply is to use high quality, protected source waters as a means of reducing the potential load of drinking water contaminants and thus reducing treatment costs and subsequent health risks to consumers. In reference [17], it was reported that the mean concentration of Cryptosporidium oocysts in protected reservoirs (0.52/100L) and pristine lakes (0.3-9.3/100L) was considerably lower compared to polluted rivers (43-60/100L) and polluted lakes (58/100L), which demonstrates the merit of this strategy. However, with increasing pressures on catchments, aquatic systems are not always sufficiently protected and pathogen risks must therefore be appropriately managed. In developing countries this is further confounded since both drinking and recreational waters may be subject to substantial direct and unregulated effluent discharges that are difficult to control at the source.