An in-depth microscopic enumeration of the dozens of species of algae present in a water column each time a lake is sampled is prohibitively costly and technically impossible for most monitoring programs. Further, in many lakes a large portion of the algal biomass may be unidentifiable by most experts (these are appropriately called LRGTs or LRBGTs -- little round green things and little round blue-green things). However, measuring the concentration of chlorophyll-a is much easier and provides a reasonable estimate of algal biomass. Chlorophyll-a is the green pigment that is responsible for a plant's ability to convert sunlight into the chemical energy needed to fix CO₂ into carbohydrates. To measure chlorophyll-a, a volume of water from a particular depth is filtered through a fine glass-fiber filter to collect all of the particulate material greater than about 1 micron (1/1000th of a millimeter) in size. The chlorophyll-a in this material is then extracted with a solvent (acetone or alcohol) and quantified using a spectrophotometer or a fluorometer.

Both chlorophyll-a and secchi depth are long-accepted methods for estimating the amount of algae in lakes. Secchi depth is much easier and less expensive to determine. However, care must be used in interpreting secchi data because of the potential influence of non-algal particulate material, such as silt from stream discharge or re-suspended bottom sediment. Also, the tea color of some lakes that's due to dissolved organic matter from bogs, can have an effect on secchi depth readings as well. Even if chlorophyll-a is measured, it may be important to also examine the algal community microscopically on occasion, since the mix of species may influence lake management decisions.