Phytoplankton succession is related to hydroclimatic conditions. In this study we provide the first description of a toxic phytoplankton succession in the Patagonian Fjord System. The shift was modulated by atmospheric-oceanographic forcing and consisted of the replacement of the marine dinoflagellate Dinophysis acuta in a highly stratified water column during austral summer by the diatom Pseudo-nitzschia calliantha in a mixed water column during late summer and early autumn. This transition, accompanied by a change in the biotoxin profiles (from lipophilic dinophysis toxins to hydrophilic domoic acid), was induced by the arrival of an intense atmospheric river. The winds in Magdalena Sound may have been further amplified, due to its west-east orientation and its location within a tall, narrow mountain canyon. This work also documents the first known appearance of toxic P. calliantha in Northern Patagonian. The potential impacts of the biotoxins of this species on higher trophic levels are discussed.