High levels of Cryptosporidium oocysts and Giardia cysts (C&G) were detected in the raw and filtered water supply in Sydney, Australia, in July and August 1998. This paper describes the results of daily monitoring in the Sydney water supply catchments between December 1998 and May 1999, as one response to that incident.

C&G were most abundant in the largest and most developed catchment. The levels of contamination in Sydney's raw water supply were of similar magnitude to raw waters in the USA and Europe, but the frequency of contamination was much lower.

Physical variables of increased stream flow and turbidity were associated with the presence of C&G. The abundance of Giardia cysts was highly correlated with the number of Cryptosporidium oocysts. Other microbial indicators of faecal contamination (faecal coliforms and C. perfringens) were not useful indicators of either C or G.

Both organisms occurred episodically in brief events, which spread rapidly through the water supply system, following stream rises in the catchment. Lake Burragorang was a poor barrier to the transfer of C&G into the bulk supply. C&G disappeared from Lake Burragorang within 4 weeks after each event. This loss rate was more rapid than predicted from settling theory. We observed settling rate of 5–10 m day−1, and postulate that sedimentation was accelerated by agglomeration of oo/cysts with other suspended particles.

A design for monitoring programmes and management action in lakes to prevent C&G entering the supply to water treatment plants is suggested.

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