Industrial wastewater is a pressing issue due to significant water and chemical usage in production, leading to the discharge of harmful micropollutants, toxins, and lethal substances into the environment without proper treatment. Employing eco-friendly biological treatment systems involving microorganisms like bacteria, fungi, and enzymes is crucial for detoxifying such contaminated water. Hence, urgent measures are needed to develop sustainable methods for treating emerging pollutants in wastewater to safeguard the environment. The toxicity of emerging pollutants poses a global environmental concern, including rare Earth elements, micro/nano plastics, antibiotics, and pharmaceuticals. Inadequate treatment systems discharge many of these hazardous compounds, challenging their detection due to their adverse effects even at low concentrations. Nano/micro-scale physical pollutants add complexity, while the fate, transport, and toxicity of these contaminants remain unclear. Understanding their behaviours and advancing remediation techniques is critical to mitigating the ecosystem exposure risks.