The burrowing amphipod, Diporeia, has declined over the past decade from one of the most abundant benthic macroinvertebrates in the Great Lakes to very low numbers in many areas. This decline parallels and may result from the recent invasion by the exotic zebra and quagga mussels (Dreissena species) and is ecologically important because Diporeia are a vital link in the food web for game fish and the fisheries in the Great Lakes. In the summer of 2000, we collected high-resolution seismic profiles, side-scan sonar profiles, and surface sediment samples along two shore-perpendicular transects from 50 to 150 m of water to investigate the sedimentological influence on the present day distribution of Diporeia in Lake Ontario. The first transect was north of Rochester NY and the other north of Olcott, NY. Sediment samples were described and split in the field, one split was analyzed for grain size (percent sand, silt and clay), organic matter, and carbonate content (by loss on ignition), and the other split was wet sieved and preserved in the field for benthic community enumeration. The preliminary results suggest that thinner and coarser postglacial muds (implying sediment resuspension and erosion) recovered from the deepest water north of Olcott appears to be a refuge for Diporeia from the invading Dreissena species.