An analytical method based on on-line SPE-LC-HESI-MS/MS has been developed for the detection and quantification of eight selected cyanotoxins in algal bloom waters that include mycrocystins, anatoxin-a and cylindrospermopsin. The injection volume was 2 mL according to the expected concentration of cyanotoxins in matrix. The method provides an analysis time of 7 min per sample, acceptable recovery values (91-101%), good precision (RSD < 13%) and method limits of detection at the sub-microgram per liter levels (0.01-0.02 μg L(-1)). A detailed discussion on optimization parameters that have an impact on the overall performance of the method are presented. In particular, method optimization permitted the chromatographic separation of anatoxin-a and phenylalanine, an isobaric interference with a similar chromatographic characteristics. All optimization and validation experiments for the on-line SPE method and chromatographic separation were performed in environmentally relevant algal bloom water matrices. The applicability of the method was tested on several algal bloom water samples from monitored lakes across the province of Québec (Québec, Canada) known to produce cyanotoxins. All of the targeted cyanotoxins were detected with the exception of cylindrospermopsin. In addition, it was found that total microcystin concentrations in several surface water samples exceeded the proposed guidelines established by the province of Québec in Canada of 1.5 μg L(-1) as well as the World Health Organization of 1 μg L(-1) for both free and cell-bound microcystin-LR equivalent.