We established an analytical method based on liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) in the precursor ion mode for simultaneous qualitative monitoring of various groups of cyanobacterial toxins. The toxin groups investigated were paralytic shellfish poisoning (PSP) toxins, anatoxins (ANAs), cylindrospermopsins (CYNs), microcystins (MCs), and nodularins (NODs), including rare and uncharacterized derivatives found in plankton and water matrices. Alternative analytical methods based on tandem mass spectrometry commonly operate in multiple reaction monitoring (MRM) mode and depend on prior knowledge of putative toxigenicity of the cyanobacterium species and strain, and the expected toxin variants. In contrast, the precursor ion mode yields diagnostic mass fragments for the detection of characteristic compounds of the different toxin classes and thus allows monitoring of a large set of unspecified cyanotoxins of various groups, even when the species composition is undetermined or uncertain. This rapid method enables screening for a wide spectrum of toxic cyanobacterial metabolites and degradation products in a single chromatographic separation with detection limits at nanogram levels. The precursor ion technique is a valuable adjunct to existing mass spectrometric methods for cyanotoxins, although it is not a complete replacement for detailed quantitative analysis requiring comprehensive sample cleanup.