The objective of this study is to demonstrate the successful functionalization of the surface of a chalcogenide infrared waveguide with the ultimate goal of developing an infrared micro-sensor device. First, a polyisobutylene coating was selected by testing its physico-chemical compatibility with a Ge-Sb-Se selenide surface. To simulate the chalcogenide platform infrared sensor, the detection of benzene, toluene, and ortho-, meta- and para-xylenes was efficaciously performed using a polyisobutylene layer spin-coated on 1 and 2.5 mu m co-sputtered selenide films of Ge28Sb12Se60 composition deposited on a zinc selenide prism used for attenuated total reflection spectroscopy. The thickness of the polymer coating was optimized by attenuated total reflection spectroscopy to achieve the highest possible attenuation of water absorption while maintaining the diffusion rate of the pollutant through the polymer film compatible with the targeted in situ analysis. Then, natural water, i.e., groundwater, wastewater, and seawater, was sampled for detection measurement by means of attenuated total reflection spectroscopy. This study is a valuable contribution concerning the functionalization by a hydrophobic polymer compatible with a chalcogenide optical sensor designed to operate in the mid-infrared spectral range to detect in situ organic molecules in natural water.