Cyanobacterial blooms increasingly impair inland waters, with the potential for a concurrent increase in cyanotoxins that have been linked to animal and human mortalities. Microcystins (MCs) are among the most commonly detected cyanotoxins, but little is known about the distribution of different MC congeners despite large differences in their biomagnification, persistence, and toxicity. Using raw-water intake data from sites around the Great Lakes basin, we applied multivariate canonical analyses and regression tree analyses to identify how different congeners (MC-LA, -LR, -RR, and -YR) varied with changes in meteorological and nutrient conditions over time (10 years) and space (longitude range: 77°2′60 to 94°29′23 W). We found that MC-LR was associated with strong winds, warm temperatures, and nutrient-rich conditions, whereas the equally toxic yet less commonly studied MC-LA tended to dominate under intermediate winds, wetter, and nutrient-poor conditions. A global synthesis of lake data in the peer-reviewed literature showed that the composition of MC congeners differs among regions, with MC-LA more commonly reported in North America than Europe. Global patterns of MC congeners tended to vary with lake nutrient conditions and lake morphometry. Ultimately, knowledge of the environmental factors leading to the formation of different MC congeners in freshwaters is necessary to assess the duration and degree of toxin exposure under future global change.