Abstract In July 1997, strong rainfall events in the upper Oder catchment area caused a flood catastrophe. This provided a unique opportunity to investigate the impacts of flood events on the Baltic Sea ecosystem. About 9 km 3 of water discharged into the Pomeranian Bight within only 5 weeks, while the normal mean water discharge of the Oder River is 18 km 3/year. The floodwaters reached the inner coastal Oder Lagoon on July 20. On July 28, low salinity (<3) and a high suspended particulate material (SPM) content (11 mg/dm 3) measured at a Baltic Sea coastal station close to the mouth of the Oder Lagoon indicated the presence of lagoon water that had been displaced by the floodwaters. In this water, about 88.9% of Hg and Cd, 94.3% of Pb, 55.5% of Co and 22.5% of Cu were associated with particles, while at the reference station 152 (Arkona Basin), this proportion was much lower (due to 10 times lower particle concentrations). On July 31, lower salinity and SPM concentrations at the coastal station indicated that the floodwaters had reached the Baltic Sea. The percentage of metals bounded to particles had decreased to 66% for Hg, 61% for Cd, 58% for Pb, 37% for Co and 11% for Cu. Compared to the summer of 1995, the mean Hg and Cd discharge during the flood increased by a factor of 4.5–5 due to the 4.5 times higher water discharge. The discharge of Pb increased by a factor of 5.5 and that of Cu and Co by a factor of 4. The inflowing water was rapidly diluted in the Pomeranian Bight, with stations more distance from the mouth of the lagoon showing much lower concentrations. A significant reverse relationship between salinity and the trace metal contents of Pb, Cu, Co and Mn demonstrated conservative mixing during the flood event. Only for dissolved cadmium (Cddiss) was a positive linear relationship with the salinity observed, which is attributed to the Cddiss uptake by the particle-rich flood waters. No elevated concentrations were measured. In conclusion, the trace metals in the floodwaters are not likely to have caused additional adverse effects in the Baltic Sea ecosystem.