Raman scattering of radiation applied to a water sample is used to assess occurrence of a pathogen in the sample. The method is useful for detecting pathogens that are difficult to detect using other methods, such as protozoa. Examples of organisms that can be detected in water samples using these methods include protozoa of the genus Cryptosporidium and the genus Giardia. The methods described herein have important applications, such as for detection of Cryptosporidium organisms in municipal water systems.