Biological treatment is the predominant method for removing and stabilizing biodegradable substances, primarily organic matter, from wastewater. This process leverages naturally occurring microorganisms, particularly bacteria, to metabolize contaminants at accelerated rates. The core of biological treatment lies in three metabolic phases: oxidation, synthesis (cell growth), and endogenous respiration (cell self-destruction). The dynamics of these processes are governed by microbial growth kinetics, which can be mathematically modeled using equations such as the Monod equation for substrate-limited growth and the Haldane equation for systems with inhibitory substances.

The effectiveness of any biological treatment system is contingent upon controlling key environmental factors, including temperature, pH, and nutrient availability. A critical operational parameter is the Food to Microorganism (M/F) ratio, which dictates the metabolic state of the microbial population and influences both treatment efficiency and sludge settling characteristics. While toxic substances can inhibit microbial activity, acclimated biological systems are increasingly utilized for treating hazardous wastes, with fixed-film reactors demonstrating particular resilience to shock loads.

Wastewater treatment configurations are broadly classified into fixed-film systems (e.g., trickling filters, Rotating Biological Contactors) where biomass grows on a stationary medium, and suspended-contact systems (e.g., the activated sludge process) where biomass is mixed with the wastewater. The activated sludge process, a cornerstone of aerobic treatment, has numerous modifications—including Step Aeration, Extended Aeration, and Completely Mixed systems—each tailored to specific loading rates and treatment objectives. Anaerobic treatment is also widely used, especially for high-strength wastes and sludges, converting organic matter into methane and carbon dioxide. Advanced biological systems can be designed for nutrient removal, employing sequential aerobic and anaerobic stages for nitrification, denitrification, and enhanced phosphorus uptake.