Pontoporeia affinis, a burrowing amphipod and the predominant macrobenthic invertebrate in the upper Great Lakes, was studied during the summer months of 1960 and 1961 with regard for its association with the bottom sediments. The primary requirement of the sampling method was to obtain an undisturbed sediment sample. A corer was used to achieve this end. The particle size distribution of the sediments in the study area is graded from coarse, well-sorted sands in the shallow water at the mouth of Grand Traverse Bay to fine, less-well-sorted sands in the deeper water of Lake Michigan. Loss on ignition was utilized to estimate the organic material in the sediments. Over the sandy sediments organic matter was largely restricted to a thin detrital layer. The amount of organic material in the silty sediments of the deep water was several times that of the sandy sediments. Bacteria were counted directly and correlated with depth, particle size, and estimates of the organic content of the sediments. The number of bacteria per gram of dry sediments ranged from 126000000 to 860000000. The distribution of P. affinis in the study area showed no signficant correlation with depth, particle size, or organic matter estimates of the sediments, but correlated with the number of bacteria in the sediments. The numbers of P. affinis collected from several of the stations exceeded maximum population densities reported in the literature. In the laboratory P. affinis selected sediments particles smaller than 0.05 mm. There was no apparent resolution of size differences in experiments utilizing sediments finer than 0.05 mm. There was significant selection of substrates whose surface layers were enriched with organic matter or which were allowed to "condition," assumedly by the growth of bacteria on the substrate surfaces. Relationships of P. affinis to the substrate were shown to be strongly influenced by the presence of bacteria and organic matter in the sediments, one or both of these serving as the energy source for the amphipod populations. The predominance of P. affinis in the benthic community and its high population densities indicate that it accounts for a large part of the energy dynamics of the benthic trophic system.