Abstract: Biological emerging 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 transmit genetic information, rendering their control considerably more challenging. Wastewater treatment systems function as both 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 the aforementioned biological emerging contaminants. Conventional secondary biological processes (e.g., oxidation ditches and anaerobic/anoxic/oxic (A/A/O) systems) can achieve 2–5 log reductions of microorganisms through biodegradation and sludge adsorption; however, residues of resistance genes and viruses are still detectable in the effluent. Membrane separation technologies effectively retain resistant bacteria and intracellular ARGs, but exhibit limited removal efficiency for extracellular ARGs and small-sized viruses (e.g., adenoviruses and noroviruses). At the molecular level, membrane separation primarily achieves 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 fragmentation and loss of gene function. AOPs (e.g., electro-Fenton and UV/O₃) can achieve 5–7 log inactivation of pathogens and ARB, 2–5 log degradation of ARGs, and 2–4 log reduction of viruses, albeit with high operational costs and limited stability. The unique challenges posed by biological emerging contaminants include their ability to proliferate, 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 parameters (e.g., temperature, pH, and hydraulic retention time). Meanwhile, coexisting pollutants such as antibiotics and heavy metals act as selective pressures, exerting synergistic effects that promote the maintenance and dissemination of resistance. Future research should focus on establishing priority control lists for high-risk contaminants (e.g., mobile ARGs, carbapenem resistance genes, and highly persistent viruses), developing synergistic multi-process control strategies, and advancing online monitoring and intelligent technologies. Promising approaches include online biosensors and soft sensors for real-time data acquisition, machine learning-based prediction and early warning models, and digital twin-based adaptive control for dynamic optimization of operational parameters in response to influent fluctuations and changes in selective pressure. These efforts will provide scientific support for the precise management of biological emerging contaminants in wastewater systems.