Microcystins (MCs) are potent cyclic-peptide toxins produced by cyanobacteria during freshwater bloom episodes. They can severely impact drinking water supplies and recreational waters. More than 300 MCs are known today, which are toxic, mainly by inhibiting protein phosphatases. MC-RR is an important congener, as shown in several bloom episodes. There are still serious gaps of knowledge regarding the reaction pathways and transformation products of MCs with reactive species which have a role in advanced oxidation processes (AOPs) or in degradation processes in natural waters. In this study, we applied the principles of radiation chemistry of water to investigate the transformations of the less-studied MC-RR by a range of oxidizing (hydroxyl radical, superoxide ion, hydroperoxyl radical) and reducing (hydrogen atom, hydrated electron) species. We manipulated a steady-state radiation-chemical system using scavengers to investigate and quantify the effects of single species. We used high-resolution mass spectrometry combined with computational and visualization platforms to annotate MS features of transformation products and to compare the single-species reaction pathways. Our results contribute to risk assessment concerning the fate of MCs in water treatment processes and in the environment.