Lake Michigan benthic macrofauna have been studied for almost a century, allowing for a unique analysis of long-term changes in community structure. We examined changes in abundances of three major taxonomic groups of benthic macroinvertebrates (Diporeia, Oligochaeta, and Sphaeriidae) in southern Lake Michigan from 1931-2015, and identified the most likely causes for these changes. Abundances of all three groups increased during 1931-1980, with the bulk of these increases occurring in nearshore (≤ 50 m) waters and coincident with increasing loading of phosphorus (P) to the lake. Abundances of all three taxa declined during 1980-2000 again mostly in nearshore waters and coincident with decreased P loading. The quagga mussel (Dreissena rostriformis bugensis) invasion was associated with a further decline in phytoplankton primary production during 2000-2015. Both Diporeia and Sphaeriidae declined in abundance during that time, with Diporeia exhibiting the more pronounced decrease of the two groups. In contrast, Oligochaeta increased in abundance during 2000-2015. The quagga mussel has become, by far, the most abundant benthic macroinvertebrate species in terms of density and biomass. Overall, the primary driver of changes in the abundances of the three major taxa during this 85-year period appeared to be changes in phytoplankton primary production due to changing P loadings and, later in the time series, Dreissena filtering. The dreissenid mussel invasions coincided with a rapid decline of Diporeia abundance, but the mechanism of this negative effect remains unidentified. In contrast, Oligochaeta likely benefitted from the quagga mussel invasion; perhaps via quagga-generated food supplies.