Surveys of the benthic macroinvertebrate community were conducted in the main basin of Lake Huron in 2000 and 2003, and in Georgian Bay and North Channel in 2002. Results were compared to surveys conducted in the 1960s and early 1970s. Although data of earlier surveys were inconsistent, our best estimates suggest that total density of the four major benthic taxa (Diporeia spp., Oligochaeta, Sphaeriidae, and Chironomidae) in the main basin declined dramatically between the early 1970s and 2000. Populations of all major taxa continued to decline between 2000 and 2003, particularly Diporeia and Sphaeriidae. Diporeia was rare or absent in the southern end of the lake and in some nearshore areas in 2000, and by 2003 was not found at depths < 50 m except in the far northeastern end of the lake. Densities of the major taxa in Georgian Bay and North Channel in 2002 were not different from densities in 1973 despite differences in survey methods. A limited study in southern Georgian Bay, however, found that densities of both Diporeia and Sphaeriidae declined to zero at most sites between 2000 and 2004. The population of Dreissena polymorpha was stable in all lake areas, but Dreissena bugensis increased, particularly at the 31–50 m depth interval in the main basin. Since there were no extensive surveys in Lake Huron in the period between nutrient abatement (late 1970s) and the establishment of Dreissena (early 1990s), it is difficult to determine relative roles of these events on observed declines. However, since phosphorus loads have been stable since the early 1980s, declines between 2000 and 2003 can likely be attributed to Dreissena.