The Gulf of Riga, river Daugava and several interconnected lakes around the City of Riga, Latvia, form adynamic brackish-freshwater system favouring occurrence of toxic cyanobacteria. We examined bioaccumulation of microcystins and nodularin-R in aquatic organisms in Latvian lakes, the Gulf of Riga and west coast of open Baltic Sea in 2002-2007. The freshwater unionids accumulated toxins efficiently,followed by snails. In contrast, Dreissena polymorpha and most lake fishes (except roach) accumulated much less hepatotoxins. Significant nodularin-R concentrations were detected also in marine clams and flounders. No transfer of nodularin-R and microcystins between lake and brackish water systems took place. Lake mussels can transfer hepatotoxins to higher organisms, and also effectively remove toxins from the water column. Obvious health risks to aquatic organisms and humans are discussed.