The Vistula Lagoon (southern Baltic Sea) is a shallow and highly eutrophic water body, with frequent blooms of cyanobacteria dominated by Microcystis and Anabaena species. Two Microcystis strains, MK10.10 and MAKR0205, isolated from the lagoon were characterised in this work. The morphology of the isolates differed significantly with respect to cell size and their ability to form aggregates. Based on the 16S rRNA sequence and 16S-23S internal transcribed spacer (ITS) sequence, both isolates were classified as Microcystis aeruginosa. However, only one isolate, MK10.10, possessed the mcy genes responsible for microcystin biosynthesis and only this strain produced microcystins. The effects of environmental factors, such as light, temperature and salinity, on toxin production turned out to be minor. Under the culture conditions used in the experiments, the biomass of the toxic MK10.10 was always lower. Hybrid quadrupole-time-of-flight liquid chromatography/tandem mass spectrometry (QTOF-LC/MS/MS) was used to elucidate the structure of the microcystin (MC) variants produced by MK10.10. Based on molecular ion and fragmentation spectra, the toxins were identified as MC-LR, MC-VR and MC-HIlR. Our study confirmed that some morphological criteria could be useful in preliminarily assessing the potential toxicity of a Microcystis bloom.