Understanding fish habitat use is important in determining conditions that ultimately affect fish energetics, growth and reproduction. Great Lakes lake whitefish (Coregonus clupeaformis) have demonstrated dramatic changes in growth and life history traits since the appearance of dreissenid mussels in the Great Lakes, but the role of habitat occupancy in driving these changes is poorly understood. To better understand temporal changes in lake whitefish depth of capture (D_w), we compiled a database of fishery-independent surveys representing multiple populations across all five Laurentian Great Lakes. By demonstrating the importance of survey design in estimating D_w, we describe a novel method for detecting survey-based bias in D_w and removing potentially biased data. Using unbiased D_w estimates, we show clear differences in the pattern and timing of changes in lake whitefish D_w between our reference sites (Lake Superior) and those that have experienced significant benthic food web changes (lakes Michigan, Huron, Erie and Ontario). Lake whitefish D_w in Lake Superior tended to gradually shift to shallower waters, but changed rapidly in other locations coincident with dreissenid establishment and declines in Diporeia densities. Almost all lake whitefish populations that were exposed to dreissenids demonstrated deeper D_w following benthic food web change, though a subset of these populations subsequently shifted to more shallow depths. In some cases in lakes Huron and Ontario, shifts towards more shallow D_w are occurring well after documented Diporeia collapse, suggesting the role of other drivers such as habitat availability or reliance on alternative prey sources.