Microcystins, anatoxins and okadaic acid are toxins produced by freshwater cyanobacteria and marine dinoflagellates. These toxins have been the responsible for the illness and death of biota and humans. To determine their presence in water during blooms, sensitive analytical methods are needed. In this study, we have developed a new liquid chromatography tandem mass spectrometry (LC-MS/MS) method for fast multiresidue determination of five toxins in suspended material and sediment samples. For each target compound, two selected reaction monitoring (SRM) transitions were optimised. Chromatographic conditions were optimised considering that the compounds analysed had different chemical structure and chromatographic behaviour. Using a Luna C18 column and specific SRM transitions, five phytotoxins were resolved. Method detection limits (MDL) for anatoxin-a, microcystins RR, LR and YR and okadaic acid were 7.1, 3.3, 81.7, 102.8 and 28.8 ng g(-1) dry weight in sediment, respectively. The developed analytical method was successfully applied to analyse the presence of toxins in suspended solids and sediment from Ebro River (NE Spain) and Ebro delta-associated lagoons. Anatoxin-a was detected downstream of the Riba-Roja reservoir with levels ranging from 20 to 1120 ng g(-1) dry weight of suspended solids. Okadaic acid was only detected in three samples collected in the Alfacs Bay (Ebro delta, Spain) affected by Dinophysis blooms in 2012.