Chlorophyll a is the green photosynthetic pigment found in plants and algae.  Measuring chlorophyll concentrations allows GBMSD to indirectly determine the abundance of phytoplankton, or algae, suspended within the water column.  Often, if a waterbody is considered to be highly productive, it has both high concentrations of chlorophyll a and nutrients, such as total phosphorus.

Excessive algae or algal blooms, often leads to reduced water clarity and light penetration.  Algal blooms can also cause oxygen depletion in the hypolimnion of a lake as dying algae decomposes.

The RAP set a target of 13 ug/l to 32 ug/l, is not being met. However, the introduction of zebra mussels has lead to a small reduction in chlorophyll a concentrations in zones 1 -3 in the Bay of Green Bay.