Microcystis spp. blooms have occurred annually in western Lake Erie since about 1995. Microcystis produce a group of toxins known as microcystins which can be harmful to livestock and to humans. In this study, surface water samples were collected from six sites during six sampling events from July to October in 2007. In situ environmental data (e.g. pH, temperature) and laboratory analyses (e.g. nutrients) were carried out to characterize the six sites. The Microcystis spp. density ranged from 102 to 107 cells/ml. Microcystin-LR concentration of 20 of all 36 samples were below the detection limit (0.15–5 ppb), while the microcystin-LR concentration in the 16 remaining samples ranged from 0.5 to 3 × 103 μg per gram dry weight. The aim of this research was to investigate the relationships between sampling location, environmental parameters, Microcystis spp. concentration, and microcystin-LR concentration. The results suggest that temperature, nutrient concentration, turbidity, and wind speed and direction (P<0.05) are factors which affected Microcystis spp. density. Sampling site 8M, located 13 m from the Maumee River, provided an advantage for Microcystis spp. growth, presumably due to intermediate water depth (5.5 m) combined with impact from the river. No relationship was found between Microcystis spp. density and microcystin-LR concentration. Temperature, nutrient concentration and DO (P<0.05) were associated with the production of microcystin-LR.