Cyanobacteria, which form water blooms all over the world, can produce a wide range of cyanotoxins such as hepatotoxic microcystins (MCs) and other biologically active metabolites harmful to living organisms, including humans. Microcystin biodegradation, particularly caused by bacteria, has been broadly documented; however, studies in this field focus mainly on strains isolated from natural aquatic environments. In this paper, the biodegradation of microcystin-RR (MC-RR), microcystin-LR (MC-LR), and microcystin-LF (MC-LF) after incubation with Spirodela polyrhiza and the associated microorganisms (which were cultured under laboratory conditions) is shown. The strongest MC biodegradation rate after nine days of incubation was observed for MC-RR, followed by MC-LR. No statistically significant decrease in the concentration of MC-LF was noted. Products of MC decomposition were detected via the HPLC method, and their highest number was found for MC-RR (six products with the retention time between 5.6 and 16.2 min), followed by MC-LR (two products with the retention time between 19.3 and 20.2 min). Although the decrease in MC-LF concentration was not significant, four MC-LF degradation products were detected with the retention time between 28.9 and 33.0 min. The results showed that MC-LF was the most stable and resistant MC variant under experimental conditions. No accumulation of MCs or their biodegradation products in S. polyrhiza was found. The findings suggest that the microorganisms (bacteria and algae) associated with S. polyrhiza could be responsible for the MC biodegradation observed. Therefore, there is a need to broaden the research on the biodegradation products detected and potential MC-degraders associated with plants.