‘Deep waters’ explains the role of François A. Forel in the birth and development of limnology, a new integrative science he defined as ‘the oceanography of lakes’. In his comprehensive monograph on Lake Geneva (1892), Forel subdivided the science of lakes into different disciplines and subjects. There were two aspects of Forel’s new science that set his thinking apart from many of his contemporaries. Studying the physical, chemical, and biological properties of lakes produced an integrated picture of the ecosystem. The second aspect recognized that human beings were also part of the ecosystem. The creation of lakes, their underwater shape, and the importance of lake sediments analysis is also discussed.