Cyanobacteria of the Baltic Sea have multiple effects on organisms that influence the food chain dynamics on several trophic levels. Cyanobacteria contain several bioactive compounds, such as alkaloids, peptides, and lipopolysaccharides. A group of nonribosomally produced oligopeptides, namely microcystins and nodularin, are tumor promoters and cause oxidative stress in the affected cells. Zooplankton graze on cyanobacteria, and when ingested, the hepatotoxins (nodularin) decrease the egg production of, for example, copepods. However, the observed effects are very variable, because many crustaceans are tolerant to nodularin and because cyanobacteria may complement the diet of grazers in small amounts. Cyanobacterial toxins are transferred through the food web from one trophic level to another. The transfer rate is relatively low in the pelagic food web, but reduced feeding and growth rates of fish larvae have been observed. In the benthic food web, especially in blue mussels, nodularin concentrations are high, and benthic feeding juvenile flounders have been observed to disappear from bloom areas. In the littoral ecosystem, gammarids have shown increased mortality and weakening of reproductive success under cyanobacterial exposure. In contrast, mysid shrimps seem to be tolerant to cyanobacterial exposure. In fish larvae, detoxication of nodularin poses a metabolic cost that is reflected as decreased growth and condition, which may increase their susceptibility to predation. Cyanobacterial filaments and aggregates also interfere with both hydromechanical and visual feeding of planktivores. The feeding appendages of mysid shrimps may clog, and the filaments interfere with prey detection of pike larvae. On the other hand, a cyanobacterial bloom may provide a refuge for both zooplankton and small fish. As the decaying bloom also provides an ample source of organic carbon and nutrients for the organisms of the microbial loop, the zooplankton species capable of selective feeding may thrive in bloom conditions. Cyanobacteria also compete for nutrients with other primary producers and change the nitrogen (N) : phosphorus (P) balance of their environment by their N-fixation. Further, the bioactive compounds of cyanobacteria directly influence other primary producers, favoring cyanobacteria, chlorophytes, dinoflagellates, and nanoflagellates and inhibiting cryptophytes. As the selective grazers also shift the grazing pressure on other species than cyanobacteria, changes in the structure and functioning of the Baltic Sea communities and ecosystems are likely to occur during the cyanobacterial bloom season.