Microbiological monitoring of water is of primary importance for preservation of human health, particularly in an arid zone like the U.S. southwest. In this work, infrared spectroscopic methods were developed to identify and quantify microorganisms present in water and water-related environmental samples. Focus of the work was primarily on evaluating the impact of various sterilization methods on microorganism physiology as gauged by the non-invasive approach of infrared spectroscopy. This work demonstrates that FTIR techniques can be used to identify changes in the physiology of microorganisms and that for heat treatment, a correlation between spectral changes and the viability of microorganisms can be made.