Freshwater Harmful Algal Blooms (HABs) pose serious risks throughout the world to drinking water, recreation, and ecosystem health. The Great Lakes, which contain nearly 20% of the world’s available surface freshwater, have been experiencing an increase in HABs since the 1990s. Knowledge gaps relating to HABs remain even after extensive and ongoing research efforts. These knowledge gaps are presented below for the benefit of water resource managers, state and federal agencies, legislators, and others involved in the development of policies to address HABs throughout the Great Lakes.