The Lake Pontchartrain Basin is a complex system of physical and biological elements. Due to the actions of man, the Basin's ecosystem has changed significantly over the past half century. These changes have impaired water quality and habitats throughout the Pontchartrain Basin. Recreational activities including swimming have been banned in areas of the lake. This paper discusses sources of microbial contamination impacting designated use criteria and the need of disinfection for water quality enhancement. Quantification of microbial loadings and identification of organisms of particular concern are made. Alternative Best Management Practices (BMPs) are suggested with emphasis on disinfection and engineered microbial reduction technologies.