Species invasion, one of the major components of global change, is projected to be the biggest driver of biodiversity change in lakes. Invasive filter-feeders are amongst the most disruptive stressors in freshwater systems globally. Most notably, invasive dreissenid mussels, commonly known as zebra and quagga mussels, are a key threat to the health of the aquatic ecosystems in North America. Once introduced, dreissenid mussels impose a strong ecological selection due to intense filter-feeding. For example: replacement of the native mussel Lampsilis by the zebra mussels in Lake St. Clair increased the fraction of the water column cleared per day from 0.03 to 0.45. As such, dreissenid mussels represent a significant layer of trophic complexity in the ecosystems they invade. Despite the fact that bacteria play an outsize role in controlling nutrient and energy fluxes in aquatic ecosystems, only a few studies have looked at the impacts of these mussels on overall bacterial abundance and biodiversity. We used 6S rRNA gene and metagenomic sequencing approaches to study the impacts of an invasive filter-feeder on freshwater bacteria. We conducted ten short-term dreissenid grazing experiments in 2019 using water from two eutrophic regions of the Laurentian Great lakes — the western basin of Lake Erie and Saginaw Bay in Lake Huron. We found that predation by dreissenid mussels led to decline in overall bacterial abundance and diversity in both lakes. However, feeding on bacteria was not observed during every experiment. We also found that traits related to feeding resistance are less phylogenetically conserved than previously thought. Our results highlight the role of temporal, spatial, and genomic heterogeneity in bacterial response dynamics to a globally important invasive filter feeder.