Microcystins (MCs) produced by cyanobacteria are a ubiquitous worldwide problem because some MCs can cause tumor formation and are hepatotoxic. In the Santa María del Oro crater lake, Mexico, plankton scums are recurrent during most of the year and are associated with cyanobacteria of the genera Microcystis spp. and Lyngbya spp. As some of these species are associated with the production of MCs and paralytic shellfish toxins (PSTs), samples from these scums and particulate matter were collected and analyzed for the main bloom species and toxins by a ultrahigh performance liquid chromatography coupled to tandem mass spectrometry (UHPLC-MS/MS) and high performance liquid chromatography with fluorescence detection (HPLC-FLD). Results showed that the main bloom-forming species were Limnoraphis robusta and Microcystis aeruginosa, the presence of at least seven MC congeners and the absence of PSTs in the algae scums. The MCs identified were MC-WR, MC-LR, MC-LA, MC-HilR, MC-LF, MC-YR, and MC-LY. On a dry mass weight basis, MC concentrations were low and ranged between 0.15 and 6.84 μg/kg. Toxin profiles were dominated by MC-WR, MC-LR, and MC-LA, representing 94.5% of the total sample, with each analog contributing 39.8%, 38.1% and 16.5% by relative concentration, respectively. Two of the more hazardous congeners, MC-LR and MC-LA, represented 54.6% of the total MC concentration. MCs in particulate matter along the depth profile were not detected. The MC profile is linked to M. aeruginosa, and it represents the first quantitative MC congener description for this species from a Mexican water ecosystem. Since these mats are recurrent yearly, their effects on humans and wild fauna, and the possible role of anthropogenic activities that favor their presence and proliferation, need to be evaluated.