Algae is a fundamental producer in the food web of freshwater ecosystems. Artificially elevated nutrient levels can cause algae to grow in excess causing ecological and aesthetic problems in lakes and streams. Algae occurs in two general patterns. One is as growth directly to the substrate called periphyton and the other is free floating in the water column called phytoplankton.

Relative amounts of algae, whether in the form of periphyton or phytoplankton can be quantified by the analysis of chlorophyll a contained in the algae in a sample. Samples for chlorophyll a (the most predominant form of chlorophyll) analysis are collected by running water through a filter. For phytoplankton, a measured amount of water from the water column is run through the filter. For periphyton, a known area from either natural or artificial substrate is scraped and rinsed through the filter. Phytoplankton chlorophyll a is reported in units of µg/L and periphyton chlorophyll a is reported in units of mg/m2.

Staff uses fluorometry methods of analyzing chlorophyll a that are similar to methods used by the University of Missouri. Before a sample can be analyzed by the fluorometer, chlorophyll a must be extracted from the filter using buffered ethanol. After the extraction process, the analysis can be conducted using the fluorometer that measures the fluorescence of wavelengths specific to chlorophyll a. A correction procedure is used to correct for byproducts in the process.