A liquid chromatography electrospray mass spectrometry (LC/ESI/MS) method working in multiple reactions monitoring mode for the determination of trace amounts of microcystin variants (MC-LR and [Dha⁷] MC-LR) in waters was developed. The limit of quantification was 0.05 μg/L and the limit of detection was 0.015 μg/L for MC-LR and [Dha⁷] MC-LR, respectively. Recoveries for MCs were in the range of 68%–81%. MC-LR and [Dha⁷] MC-LR were chemically stable with similar physiochemical behavior.