AbstractThe brackish water cyanobacterium Nodularia spumigena regularly forms waterblooms in the Baltic Sea. Many N. spumigena strains can produce nodularin, a hepatotoxic penta‐peptide, which has caused several animal poisonings in the Baltic Sea area. To improve our understanding of nodularin bioaccumulation in aquatic organisms this study measured nodularin in flounder and cod caught from the Baltic Sea. Flounders were collected from the western Gulf of Finland in July 1996, September 1997, and September 1998, and from the Gulf of Bothnia in August 1997 and September 1998. Flounders were also collected from the coastal areas of Sweden in the Baltic Proper during September 1998. Cod were caught from the southern Baltic Sea in August 1998. Livers and muscles of the 1997 fish were isolated, extracted, and analysed for nodularin using high‐performance liquid chromatography (HPLC) and enzyme‐linked immunosorbent assay (ELISA) and protein phosphatase 1 (PP1) inhibition assay. Approximately 30–70 ng of nodularin/g dry weight (maximum value 140 ng/g) were found in the liver tissue samples by ELISA and PP1 inhibition. These concentrations were below the detection limit of HPLC. PP1 assay showed inhibition also in muscle samples, but this may due to other compounds present in the muscle extracts rather than NODLN or due to matrix interference. The recovery of nodularin from liver tissue with ELISA and PP1 assays was about 30%. Nodularin concentrations in samples are not corrected for recovery. Although the concentrations of nodularin found in this study are low further studies of nodularin are needed to assess possible bioaccumulation in brackish water food webs. © 2001 John Wiley & Sons, Inc. Environ Toxicol 16: 121–126, 2001