Abstract A cyanobacterial bloom in the Gulf of Finland, Baltic Sea, was sampled throughout the development and senescence of aggregates in August 1999. While conditions inside the aggregates were favourable for denitrification (rich in nitrogen and carbon, with anoxic microzones), essentially none was detected by a sensitive isotope pairing method. Polymerase chain reaction-based methods, targeting functional genes encoding the key enzymes of denitrification and nitrification processes (nirS, nirK, amoA), revealed that the non-aggregated filaments harboured amoA gene fragments with high similarity to Nitrosospira amoA sequences, as well as both types of nitrite reductase genes, nirS and nirK. Only the nirS-type nitrite reductase gene and no amoA was detected in aggregated filaments. Thus, despite optimal environmental conditions and genetic potential for denitrification, the blooms of filamentous nitrogen-fixing cyanobacteria must be seen solely as a source, and not as a sink of nitrogen in the Baltic Sea.