Invasive quagga mussels have recently replaced zebra mussels as the dominant filter-feeding bivalves in the Great Lakes. This study examined microzooplankton (i.e., grazers < 200 μm) and their trophic interactions with phytoplankton, bacteria, and bivalve mussels in Saginaw Bay, Lake Huron, following the zebra to quagga mussel shift. Microzooplankton distribution displayed strong spatial and temporal variability (1.73–28.5 μg C/L) relative to phytoplankton distribution. Ciliates were the dominant component, especially in the spring and early summer. Rotifers and dinoflagellates increased toward late summer/fall in the inner and outer parts of the bay, respectively. Microzooplankton grazing matched bacterial growth rates and removed ca. 30% of the phytoplankton standing stock in the < 100 μm size fraction per day. The greatest herbivory occurred at the site dominated by colonial cyanobacteria. Microzooplankton, which comprised < 4% of the quagga mussels prey field (i.e. available prey), contributed 77% and 34% to the quagga carbon-based diet during Microcystis and diatom blooms, respectively. Feeding on microzooplankton could buffer mussels during lean periods, or supplement other consumed resources, particularly during noxious cyanobacterial blooms. The results of this study demonstrate that microzooplankton are a resilient and critical component of the Saginaw Bay ecosystem.