Onondaga Lake in Syracuse, NY, is recovering from a century of industrial and municipal pollution. The distribution and diversity of aquatic macrophytes have increased significantly in the past decade, and the plants currently cover 80% of the littoral area. To assess the effects of aquatic vegetation on aquatic biota, we employed quantitative sampling to examine associations of epiphytic macroinvertebrates in 4 assemblages of submerged aquatic vegetation in Onondaga Lake in 2010 and 2011. Two assemblages were predominantly monocultures—one of Stuckenia pectinata (Sago Pondweed) and the other of Chara sp. (stonewort). The third was dominated by Potamogeton foliosus (Leafy Pondweed) and Potamogeton pusillus (Small Pondweed), and the fourth was a heterogeneous community that included Ceratophyllum demersum (Coon's Tail), Myriophyllum spicatum (Eurasian Watermilfoil), and Elodea canadensis (Canadian Waterweed). Measures of invertebrate community composition—which included taxa richness, ETO richness, family richness, and NCO richness—were not consistently different in any particular macrophyte assemblage. Overall densities of epiphytic macroinvertebrates were similar to or higher than those reported in other quantitative studies of epiphytic macroinvertebrates. We found differences in the abundance of specific macroinvertebrate taxa associated with a particular macrophyte assemblage. Stonewort and the heterogeneous beds supported a similar community of gastropods and amphipods in both years, which was distinct from the high densities of Oligochaeta and Chironomidae associated with Sago Pondweed. Our observations suggest that the current distribution of aquatic macrophytes and the high density of associated macroinvertebrates provide abundant prey for sizable populations of fishes and waterfowl that prey on macroinvertebrates.