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Monitoring water quality by detecting chemical and biological contaminants is critical to ensuring the provision and discharge of clean water, hence protecting human health and the ecosystem. Among the available analytical techniques, infrared (IR) spectroscopy provides sensitive and selective detection of multiple water contaminants. In this work, we present an application of IR spectroscopy for qualitative and quantitative assessment of chemical and biological water contaminants. We focus on in-line detection of nitrogen pollutants in the form of nitrate and ammonium for wastewater treatment process control and automation. We discuss the effects of water quality parameters such as salinity, pH, and temperature on the IR spectra of nitrogen pollutants. We then focus on application of the sensor for detection of contaminants of emerging concern, such as arsenic and Per- and polyfluoroalkyl substances (PFAS) in drinking water. We demonstrate the use of multivariate statistical analysis for automated data processing in complex fluids. Finally, we discuss application of IR spectroscopy for detecting biological water contaminants. We use the metabolomic signature of E. coli bacteria to determine its presence in water as well as distinguish between different strains of bacteria. Overall, this work shows that IR spectroscopy is a promising technique for monitoring both chemical and biological contaminants in water and has the potential for real-time, inline water quality monitoring.