The ability of established populations of the non-native zebra mussel (Dreissena polymorpha) to influence phytoplankton communities and promote Microcystis aeruginosa, a potentially toxic cyanobacterium, has been reported by Fahnenstiel et al. (1995), Vanderploeg et al. (2002) and others, in the Great Lakes region. This study documents changes following zebra mussel establishment in six low-nutrient inland lake basins in northwest lower Michigan (Leelanau County). Shifts in phytoplankton communities that occurred only in basins with zebra mussels included declines in spring diatoms and chrysophytes prior to blooms of cyanobacteria. Decreases in these taxa support a competitive release hypothesis for M. aeruginosa dominance. It should also be noted that study basins did not experience increases in phosphorus or summer temperatures. M. aeruginosa proliferation may be related to zebra mussel filtering behavior, a combination of total zebra mussels and lake morphology. Zebra mussel populations were estimated using underwater video, M. aeruginosa densities were quantified from surface water and lake bathymetry and basin-wide zebra mussel densities were estimated using ArcGIS. Underwater video ground-truthed using SCUBA was an effective, yet labor intensive method to estimate zebra mussel populations, and kernel interpolation provided acceptable zebra mussel density estimates basin-wide. The relationship between M. aeruginosa density and zebra mussel filtering capacity was not significant, however the sample size may have been an issue. Microcystin (MC), the hepatotoxin produced by M. aeruginosa and other cyanobacteria, was measured before and after blooms of M. aeruginosa over depths and across seasons in whole water, sediment, macroinvertebrates, bivalves and fishes, using enzyme linked immunosorbent assay. A subset of sediment and Hexagenia spp. samples were analyzed using high performance liquid chromatography and mass spectrometry for microcystin-LR. MC was present in all components, including spring samples prior to M. aeruginosa blooms and exceeded the recreational and total daily intake guidelines of the World Health Organization in whole water (on at least one occasion) and in fish white muscle, for consumption by men, women and children. Hexagenia spp. and walleye contained the highest concentrations of MC. MC should be monitored in these lake basins because of the potential risk of chronic sub-lethal exposure to humans.