We measure chlorophyll concentration with a fluorometer, a submersible instrument that sends a beam of blue light into the water and measures the amount of red light produced by chlorophyll in the suspended algae (chlorophyll is the primary photosynthetic pigment of plants; it emits red light fluorescence when it is activated by blue light). The instrument is calibrated each sampling date by taking water samples and measuring the true chlorophyll concentration. We collect samples onto filters, extract the chlorophyll in acetone, and measure its concentration from the absorbance of light measured in a fluorometer. This plot shows the agreement between the discrete ("true") measures and those estimated from the fluorometer. This plot shows all the measurements made in South Bay during 1996. The average deviation between calculated chlorophyll (from the fluorometer) and measured chlorophyll is 0.8 milligrams per cubic meter, equivalent to a mean error of 14%.

See examples of chlorophyll a vertical profiles and time series.