The environment is being heavily impacted by the release of toxic substances due to urbanization, industrial activities, and population growth, especially affecting water bodies such as rivers, lakes, and groundwater. These toxic substances, known as micropollutants, are present in different concentrations, ranging from nanograms to milligrams per liter, depending on the water source. Micropollutants commonly include pharmaceuticals, pesticides, and endocrine-disrupting chemicals (EDCs), among others. Their presence in aquatic environments poses significant risks to ecosystems and human health, potentially leading to reproductive disturbances in fish. Research efforts have primarily focused on a limited range of micropollutants due to economic and technological constraints, hindering a comprehensive assessment of water quality and the broader ecological impacts of various pollutant types. It is crucial to broaden the scope of micropollutant screening for effective environmental monitoring. Advanced analytical methods are crucial for achieving this goal. Techniques such as gas chromatography-mass spectrometry (GC–MS), liquid chromatography-mass spectrometry (LC–MS), Fourier transform infrared (FTIR), and nuclear magnetic resonance (NMR) spectroscopy are utilized for their precision and sensitivity. However, these methods encounter difficulties in detecting mixtures of micropollutants with different chemical properties. The complexity of environmental samples often introduces matrix interferences, making accurate detection more challenging. It is essential to develop more refined techniques to effectively identify and quantify micropollutants, thus mitigating their bioaccumulative effects and safeguarding both aquatic ecosystems and human health.