Cyanobacterial blooms pose health risks to recreational water users. In New Zealand, cyanobacteria biovolumes are used to assess risk, but analyses can be time-consuming and costly. In this study, measurements from a handheld phycocyanin sensor (Cyclops-7, Turner Designs, USA) were compared with biovolumes from five lakes and a river in the Rotorua district over two years (2016, n = 121; 2017, n = 63). In the laboratory, relationships between sensor phycocyanin and biovolumes were assessed for four species to investigate precision and detection limits. The relationship between phycocyanin and biovolume was generally weak (<R2 = 0.4) and varied among lakes and years, except at high biovolumes. Precision and detection limits differed among species. The biovolume detection limit derived from relationships with phycocyanin was above alert level thresholds for two of the four cyanobacteria species assessed. The phycocyanin sensor that was tested likely has limited utility but may be useful for on-site confirmation of exceedances of alert level thresholds corresponding to when authorities should immediately issue health warnings.