The U.S. Geological Survey, in cooperation with Virginia Department of Environmental Quality, is conducting two studies to better understand the drivers of harmful algal blooms (HABs) in Lake Anna and the upper Shenandoah River Basin in Virginia. Excessive algae in streams and lakes may adversely impact the ecosystem, reduce the water quality, and, if toxigenic cyanobacteria are present, produce cyanotoxins that can pose health risks to humans and wildlife. Nutrient and sunlight are well documented drivers of HABs, however, the interaction among these and other potential factors influencing HAB growth is less understood. The focus of the presentation is to give an overview of the intensive and extensive monitoring programs that have been established, unique to each study area. The monitoring program evaluates the hydrology, geochemistry, climate, stream metabolism, community dynamics, and environmental DNA and RNA to identify the potential factors and interactions during HAB formation, persistence, and decline in these systems.