Algal studies are valuable in water quality assessment because of their importance in aquatic ecosystems and sensitivity to changes in habitat conditions. Recent advances in algal ecology and sample analysis enable the designing of research that more directly reveals patterns of algal community structure and function that are pertinent to different kinds of environmental perturbations. In addition, advances in quantitative algal ecology enable more accurate interpretation of the importance of environmental perturbations on algal community structure and function. This paper incorporates recent advances in algal ecology into suggestions on how to design algal research for water quality assessment and methods for sample analysis, presents statistical techniques which can be useful for analyzing results, and reviews interpretations of the results.