I define Environmental Biotechnology as “managing microbial communities to provide services to society.” Those services include improving water quality, producing renewable resources, and improving human health. Environmental Biotechnology creates ideal partnerships between humans and microorganisms. Environmental Biotechnology is a highly inter-disciplinary field, but at its core is the scientific discipline of microbial ecology. I briefly review the amazing advances in microbial ecology that are helping propel environmental biotechnology forward at a rapid pace. Most importantly, managing microbial communities requires innovative reactor systems and the use of new materials, including active surfaces onto which the microorganisms can accumulate and carry out their unique metabolism. To illustrate the value of innovative reactor systems, I show two examples of the active-management approach: the H2-based membrane biofilm reactor (MBfR) and microbial electrochemical cells (MxCs). The MBfR allows us to detoxify the large number of oxidized water contaminants, such as nitrate, perchlorate, selenate, and metals. The MxCs allow us to convert the biochemical oxygen demand of organics waste streams (such as food and animal wastes) to highly valuable energy outputs, particularly hydrogen gas (H2).