Cyanobacterial and algal toxins comprise a large group of harmful metabolites, belonging to different chemical classes, with a variety of chemical structures, physicochemical properties and toxic activities. In this study, a fast, simple and sensitive analytical method was developed for the simultaneous determination of multi-class cyanobacterial and algal toxins in water. The target compounds were: Cylindrospermopsin, Anatoxin-a, Nodularin, 12 Microcystins ([D-Asp3]MC-RR, MC-RR, MC-YR, MC-HtyR, [D-Asp3]MC-LR, MC-LR, MC-HilR, MC-WR, MC-LA, MC-LY, MC-LW and MC-LF), Okadaic acid and Domoic acid. Analytes were determined using liquid chromatography-tandem mass spectrometry (LC-MS/MS). A dual Solid Phase Extraction (SPE) cartridge assembly was applied for the extraction of target compounds from water. Optimized SPE parameters included cartridge material, initial sample pH, sequence of the cartridges in the SPE assembly as well as composition and volume of the elution solvent. The method was validated, providing acceptable mean recoveries and reproducibility for most analytes. Limits of detection were at the ngL(-1) level. The method was successfully applied in real lake water samples from Greece, where a wide range of Microcystins were detected for the first time, at concentrations ranging from 0.034 to 63μgL(-1).