The purpose of a secondary wastewater treatment is to remove soluble organics and suspended solids that escape the primary treatment. These removals are typically achieved by biological treatment processes. Although, conventional biological treatment may remove 85%–90% BOD5 and TSS, it does not achieve significant amounts of nitrogen and phosphorus removals. Recent advancements in the biological waste treatment technology are capable of providing enhanced organics and nutrients removals. The following topics are discussed in this chapter: biological waste treatment, microorganisms in biological waste treatment, microbial growth kinetics and substrate removal, combined suspended and attached growth reactors, environmental requirements, aerobic, anoxic and anaerobic reactors, biological nutrient removal, and theory and design examples of biological waste treatment.