This study was to investigate the metabolic characteristics of cyanobacteria in organic waste-treatment systems in order to gain a better understanding of their physiological contributions during biological waste-treatment. This in turn would provide some valuable insight into the role of cyanobacteria in the microbial community as well as their potential impact on waste-treatment efficiency. Nostoc muscorum, Synechococcus PCC7942, Spirulina platensis and Anabaena cylindrica have varying tolerance potential to organic compounds and the order of tolerance was almost same in all the strains. We have found that under organic stress, the PSII electron activity also considerably changed. The results agrees that the FIR is a good stress indicator for the four cyanobacteria, Nostoc muscorum, Synechococcus PCC 7942, Spirulina platensis and Anabaena cylindrica, and may be applied in remote sensing of the physiological state of cyanobacteria via LICF or to detect stress event. Proteins involved in the stress inhibition can be studied more. These studies provide insights to design a biosensor.