The fluorescein diacetate (FDA) assay has been widely used to measure metabolic activity in phytoplankton. It was found that FDA fluorescence values did not decrease in some stressed cells, demonstrating that the applicability of the method needs to be assessed further in the context of growth-influencing conditions. In the present study, changes of FDA fluorescence values were studied in bloom-forming cyanobacterial Microcystis aeruginosa Kutz cells under stress conditions such as nitrogen (N) or phosphorus (P) deficiency, or darkness and low temperature (10 degrees C), respectively. The results demonstrated that esterase activity decreased immediately in dark-stressed cells, which correlated with the decline of biomass and photosynthetic activity. Under the other three stress conditions, however, especially at low temperature, the cells lost photosynthetic activity but had the highest esterase activity, which was five times higher than the control group. These findings contrast with the assay criteria that the expression of a stain should reflect the change of photosynthetic activity and that stressed cells should have a lower staining intensity than the control cells. According to these results, the esterase activity response was dependent on environmental factors. Furthermore, higher fluorescence intensity did not mean higher metabolic activity, but a discrepant value indicated a severe stress.