Concentrations of a cyanobacterial toxin, nodularin, were measured in the Baltic Sea in 1998 and 1999. Statistical associations of nodularin concentrations with environmental factors were tested by multiple regression analysis. To reveal the toxin-producing organism, colonies of Aphanizomenon and filaments of Nodularia were picked and analyzed for peptide toxins. It was also investigated whether there was an association with zooplankton and Nodularia. All the measured seston samples contained nodularin, but other toxins were not detected by the HPLC analysis. In both years, the highest nodularin concentrations were found at the surface water layer. The nodularin concentrations were positively correlated with silicate concentrations in water. High concentrations of silica in surface water may indicate recent upwelling, which in turn renders surface water rich in nutrients. This upwelling is likely to intensify cyanobacterial growth and toxin production, which may explain this rather unexpected result. The picked Aphanizomenon colonies did not contain nodularin and the dissolved nodularin concentrations were below detection limit. Thus it was concluded that most of the nodularin was bound to Nodularia cells. The abundances of zooplankton (copepods, rotifers, and cladocerans) were unrelated to Nodularia, but were positively associated with Aphanizomenon.