A YSI EXO2 water quality sonde fitted with fluorometric sensors for chlorophyll-a (Chl-a) and phycocyanin (CPC) was used to determine its applicability in cyanobacterial quantification in three small urban ponds in Sydney, Australia displaying considerable variations in cyanobacterial community composition and abundance, as well as eukaryotic algae, turbidity and chromophoric dissolved organic matter. CPC and Chl-a measured in situ with the instrument was compared against laboratory measures of cyanobacterial biovolume over two summer sampling periods. A good correlation was found between CPC and total cyanobacterial biovolume in two of the three ponds. The poor correlation in the third was due to the frequent dominance of picoplanktonic sized cyanobacteria. CPC did not correlate well with cell counts, and Chl-a was a poor measure of cyanobacterial presence. The relationship between CPC measured by fluorometry varied according to the dominant cyanobacterial taxa present in the ponds at any one time. Fluorometry has good potential for use in environmental monitoring of cyanobacterial biovolume, but may need to be based on predetermined relations applicable to local water bodies. Management guidelines based on CPC concentrations would also enhance the usefulness of in situ CPC measurements.