This chapter reviews secondary biological wastewater treatment methods, emphasizing processes that reduce organic matter, suspended solids, and nutrients after primary treatment. It outlines suspended and attached growth systems, microbial metabolism pathways (aerobic, anaerobic, anoxic), and the principles of biokinetics for system design. The activated sludge process is discussed in detail, covering its configurations, operational parameters, advantages, and limitations. Biological nutrient removal through nitrification–denitrification and enhanced biological phosphorus removal is highlighted for achieving complete nutrient removal without chemicals. Anaerobic bioreactors such as UASB, CSTR, and AFBR are described, focusing on their energy efficiency and biogas production. The chapter also examines secondary clarification, membrane bioreactors, and their benefits, challenges, and advances, including hybrid systems. Finally, it addresses effluent disinfection methods like chlorination, ozonation, and UV emphasizing their mechanisms, operational considerations, and environmental implications for safe wastewater reuse or discharge.