Geosmin and 2-methylisoborneol are secondary metabolites expressed by a variety of organisms that are responsible for off-flavors in public water supplies, aquaculture, and a host of other important products. Hence, there is continuing research into the causes for their expression and methods to mitigate it, which require sensitive and accurate detection methods. In recent years, several new techniques for collecting and concentrating volatile and semi-volatile compounds have been automated and commercialized, making them available for use in most laboratories. In this study, we compared solid-phase microextraction (SPME) and membrane-assisted solvent extraction (MASE) for the detection of 2-methylisoborneol and geosmin in aqueous samples. SPME is the most sensitive of these techniques with a limit of detection of 25 parts-per-trillion for 2-methylisoborneol and 10 parts-per-trillion for geosmin but with a large relative standard deviation. MASE is less sensitive, but provides a greater level of precision, as well as the ability for multiple injections from the same sample.