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Benthic surveys were conducted in the southern basin of Lake Michigan and throughout the lake to assess trends in benthic populations, emphasizing recent changes in densities of the benthic amphipod Diporeia spp. and dreissenid mussels. In the southern basin, Diporeia populations declined 89%, 91%, and 45% between 1993 and 2002 at sites <30, 31–50, and 51–90 m, respectively. Lakewide, the population declined 65% between 1994–1995 and 2000. Over the same time period, dreissenid densities, particularly Dreissena bugensis, increased. Intensive studies at 45 m sites in the southeastern region examined changes in lipid content, age structure, and benthic food inputs relative to the hypothesis that food limitation was a factor in Diporeia's disappearance. As Diporeia densities declined to zero, length–weight remained unchanged, and lipid content generally increased. Recruitment still occurred, but the young did not survive to become adults. Based on organic carbon, biogenic silica, and chlorophyll collected in sediment traps and found in the upper sediments, pelagic inputs to the benthic region still occurred. Our field observations and laboratory experiments did not disprove the hypothesis that food limitation from dreissenid filtering activities was the cause of the decline, but direct relationships between the loss of Diporeia and indicators of food availability were difficult to establish.

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