Benthic algal communities abound in most aquatic habitats containing sunlit substrata. The species richness and physiological diversity within this community render it an excellent choice for water quality monitoring. As with any monitoring program, care must be exercised to collect data of high quality that are truly reflective of the environment to be monitored. It is also important to remember that the interface of the abiotic environment and the benthic algae is not isolated from the remainder of the aquatic community and that changes in the benthic algal community induced from chemical changes in the habitat may be modifed or masked by other factors. For example, point sources of nutrients may result in increased benthic algal productivity with little increase in benthic algal biomass because or rapid transfer of organic matter to grazers. These types of top-down forces that mask benthic algal response have been well documented in several aquatic ecosystems. Thus, benthic algal monitoring data are most valuable when combined with a suite of monitoring data including physical and chemical measurements and analysis of other biota of aquatic communities such as invertebrates.