This research explores the potential use of microwave energy to detect various substances in water, with a focus on water quality assessment and pathogen detection applications. There are many non-thermal effects of microwaves on microorganisms and their resonant frequencies could be used to identify and possibly destroy harmful pathogens, such as bacteria and viruses, without heating the water. A wide range of materials, including living organisms like Daphnia and Moina, plants, sand, plastic, and salt, were subjected to microwave measurements to assess their influence on the transmission (S21) measurements. The measurements of the living organisms did not display distinctive resonant frequencies and variations in water volume may be the source of the small measurement differences. Conversely, sand and plastic pellets affected the measurements differently, with their arrangement within the test tube emerging as a significant factor. This study also explores the impact of salinity on measurements, revealing a clear pattern that can be modeled as a series RLC resonator. Although unique resonant frequencies for the tested organisms were not identified, the presented system demonstrates the potential for detecting contaminants based on variations in measurements. Future research may extend this work to include a broader array of organisms and enhance measurement precision.