A Yellow Springs Instruments water quality sonde fitted with fluorometric probes for phycocyanin and chlorophyll a was trialled at sites along the Murray and Lower Darling Rivers, Australia, during 2008–2009. The project examined whether the in situ quantification of phycocyanin by fluorometry could be used to determine the abundance of cyanobacteria present. Abundance was measured in the laboratory as biovolume from samples collected at the same time as the phycocyanin measurements. The study found a strong positive relationship between the two measurements. However, it was found that the use of in situ phycocyanin fluorometry was not effective in turbid water higher than 50 Nephelometric turbidity units (NTU) as this produced false-positive readings for phycocyanin. There was a considerable amount of variance within the data, much probably caused by error in estimating cyanobacterial biovolumes. Some variability may also be attributed to error involved in the in situ measurement of phycocyanin, especially when cyanobacterial abundance was close to the lower limit of quantification of the instrument. This is likely to be greatest when total cyanobacterial biovolume is less than 0.4 mm3 L−1. The relationship between phycocyanin measured in situ by fluorometry and total cyanobacterial biovolume varied spatially between sites along the Murray River, probably caused by differences in cyanobacterial abundance and in the species composition of the cyanobacterial communities in different sections of the river. No relationship was found between total cyanobacterial biovolume and chlorophyll a measured by in situ fluorometry. However, in situ fluorometry has the potential to be a useful rapid assessment tool for cyanobacterial bloom management. Copyright © 2012 John Wiley & Sons, Ltd.