A key goal of zero-discharge aquaponic systems is the minimization of solids discharge from the facility. This is generally accomplished using bacterial processes to degrade or mineralize organic material (uneaten fish food, fish feces, etc.). Successful mineralization depends on heterotrophic bacteria present in sufficient quantities operating either aerobically or anaerobically. Aerobic digestion depends on large amounts of aeration to maintain high oxygen levels and prevent the creation of foul odors and bulking of solids. Anaerobic mineralization is enticing as it can result in more stable water conditions (higher pH, increased alkalinity) but there is a greater chance of system failure due to the production of nitrite or hydrogen sulfide. The bacterial processes occurring in aquaponic systems are subject to many myths and misconceptions including the bacteria species responsible, how fast they may react to changing conditions and what conditions will promote which bacteria. A framework of basic knowledge regarding aquatic microorganisms in aquaponic systems will be presented along with methods for introducing and maintaining beneficial bacteria to the system. A better understanding of the microorganisms will allow operators to more efficiently manage their systems saving time, money and resources.