Free ammonia (FA) can pose inhibitory and/or biocidal effects on a variety of microorganisms involved in different biological wastewater treatment process, which is widely presented in wastewater treatment plants (WWTPs) due to the high levels of ammonium in the systems. This review article gives the up-to-date status on several essential roles of FA in biological wastewater treatment processes: the impacts of FA, mechanisms of FA roles, modeling of FA impacts, and implications of FA for wastewater treatment. Specifically, the impacts of FA on both wastewater and sludge treatment lines were firstly summarized, including nitrification, denitrification, anaerobic ammonium oxidation (Anammox), enhanced biological phosphorus removal and anaerobic processes. The involved mechanisms were then analyzed, which indicated FA inhibition can slow specific microbial activities or even reconfigure the microbial community structure, likely due to negative impacts of FA on intracellular pH, specific enzymes and extracellular polymeric substances (EPS), thus causing cell inactivation/lysis. Mathematical models describing the impact of FA on both wastewater and sludge treatment processes were also explored to facilitate process optimization. Finally, the key implications of FA were identified, that is FA can be leveraged to substantially enhance the biodegradability of secondary sludge, which would further improve biological nutrient removal and enhance renewable energy production.