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Elevated levels of cyanobacteria were first detected near Warragamba Dam wall on 6 August 2007, which subsequently developed into a bloom during August and September and persisted in Warragamba Reservoir until December 2007. The bloom was predominantly composed of a single Microcystis species, which was shown to be potentially toxigenic, although the presence of toxins in the water was insignificant.

In the past 27 years, elevated chlorophyll-a events (with peak concentrations greater than 5 ug/L) have occurred 29 times at the dam wall. These predominantly occurred in the months of September and October. Most were attributed to green algae; however five of these occurrences have had significant cyanobacterial presence. The bloom in 2007 was approximately ten-fold larger in cell concentration than ever experienced at this site in the past.