We developed a selective method for determining N,N-dimethyldodecylamine (DMDA) and N,N-dimethyloctadecylamine (DMOA) concentrations in river and sea water samples using liquid chromatography/tandem mass spectrometry (LC/MS/MS). DMDA and DMOA are suspected to be toxic, and DMDA is categorized as a "Class I Designated Chemical Substance" under the "Act on Confirmation, etc. of Release Amounts of Specific Chemical Substances in the Environment and Promotion of Improvements to the Management Thereof" in Japan. The analytes are extracted from a water sample using solid phase extraction and the extract is evaporated and dissolved in 1 mL methanol for LC/MS/MS analysis. We analyzed DMDA and DMOA in real water samples and found that the analyte peaks were resolved effectively. The method detection limits for DMDA and DMOA were 4.7 and 0.80 ng/L, respectively.