Drift algae, especially potamoplankton, have seldom attracted limnologists’ interests in Japan, where rivers are characterised by short channels flowing down steep gradients. However, we cannot disregard planktonic algal production in rivers to understand the current Japanese river environment because many rapid streams have been artificially converted to gently flowing or stagnant waters through dam and barrage construction. In this study, I present a historical review of the literature on drift algae in Japan, with a special focus on public concerns related to drift algae in two cases, “Nagara river mouth barrage construction” and “Agano river mercury poisoning (Niigata-Minamata disease).” In the former case, the development of a potamoplanktonic population,and in the latter case, the drift and sedimentation of attached algae polluted by mercury at the upper source of pollution, were the lawsuit issues. The scientific understanding did not deepen among the stakeholders involved because of scarce information on drift algae and its mistaken notion commonly held not only by limnologists but also by administrations, lawyers, and the agencies responsible for the projects or damage. Although court decisions were declared for both lawsuits, scientific revelations remained insufficient.