Abstract: Emerging biological contaminants (e.g., pathogenic bacteria, antibiotic-resistant bacteria ARB, antibiotic resistance genes ARGs, and viruses) pose significant threats to ecosystems and public health due to their environmental persistence and potential for human infection. Unlike conventional chemical pollutants, these biological agents can replicate and transfer genetic information, rendering their control considerably more challenging. Wastewater treatment systems serve as major sinks and sources of these contaminants, necessitating a systematic evaluation of their removal efficiency and underlying mechanisms. This review systematically summarizes the performance of typical wastewater treatment processes in removing these emerging biological contaminants. Conventional secondary biological processes (e.g., oxidation ditches and anaerobic/anoxic/oxic A/A/O systems) can achieve 2–5 log reduction of microorganisms through biodegradation and sludge adsorption; however, residual resistance genes and viruses remain detectable in the effluent. Membrane separation technologies effectively retain resistant bacteria and intracellular ARGs, but exhibit limited removal efficiency for extracellular ARGs and small viruses (e.g., adenoviruses and noroviruses). Mechanistically, membrane separation relies primarily on physical retention without inactivating genetic material, whereas advanced oxidation processes (AOPs) generate reactive oxygen species (e.g., hydroxyl radicals) that attack DNA structures, leading to cleavage and loss of gene function. Consequently, AOPs (e.g., electro-Fenton and UV/O₃) can achieve 5–7 log inactivation of pathogens and ARB, a 2–8 log degradation of ARGs, and a 2–4 log reduction of viruses, albeit with high operational costs and limited stability. The unique challenges posed by emerging biological contaminants stem from their proliferative capacity, low infectious doses, and the risk of horizontal gene transfer. Removal efficiency is governed by multiple factors, including water quality characteristics (e.g., organic loading and ammonia nitrogen) and operational conditions (e.g., temperature, pH, and hydraulic retention time). Additionally, coexisting pollutants such as antibiotics and heavy metals exert selective pressures, promoting the maintenance and dissemination of resistance through synergistic effects. Future research should prioritize establishing control lists for high-risk contaminants (e.g., mobile ARGs, carbapenem resistance genes, and persistent viruses), developing synergistic multi-barrier strategies, and advancing smart, online monitoring technologies. Promising directions include online biosensors and soft sensors for real-time data acquisition, machine learning-based early-warning models, and digital twin-based adaptive control to dynamically optimize operation against influent fluctuations and shifting selective pressure. Overall, these advances will provide scientific support for the precise management of emerging biological contaminants in wastewater infrastructure.