Professor Baumgartner designs, supervises and undertakes research into various aspects of the biology and ecology of freshwater fish and systems. His interests are fish passage and fish migration, the impact of human disturbance on aquatic ecosystems, developing solutions to global challenges in water resource management and the connections between people and inland fish.
Recently he has developed a series of short-courses which aim to help organisations build capacity in specific areas of water management. Much of his work is applied and has fed back into adaptive management strategies which have resulted in state, national and international water policy development.
His main geographic areas of expertise are South-Eastern Australia, the Murray-Darling Basin and the Lower Mekong but he also has active collaborations in South Africa, Europe, North America and Indonesia.