The seven African Great Lakes are some of the most critical freshwater, large-lake systems in the world, providing essential services, food, drinking water, and other livelihood support to over 62 million people. Like most freshwater systems around the world, these lakes are strained by anthropogenic stressors, leading to degradation of these biologically important, and human-dependent resources. Despite their importance, these lakes suffer from insufficient research approaches which are short-term, disparate, and unharmonized. Further, a lack of monitoring, data and information exchange, education and training, and gender balance in research, all lead to insufficient knowledge on which to better manage and protect these lakes. While past efforts have resulted in some knowledge accumulation, there is a need for new approaches to understanding and managing these lakes: bottom-up, harmonized, and long-term processes. This paper, and those within this special section of the Journal of Great Lakes Research, highlight new, highly collaborative efforts of freshwater experts representing each riparian country of each African Great Lake through formal advisory groups. These papers are the result of harmonized efforts and collegial agreements as to what issues need to be addressed foremost, written by those on the ground. While each lake has specific, prioritized lists of issues, five overarching issues must be addressed to achieve success on these lakes: providing agency and coordination of African freshwater scientists; increase long-term monitoring; strengthen education and training of existing and future experts; enhance information and data exchange; and ensure stronger gender balance in science and leadership positions.