Declines in recruitment of lake whitefish (Coregonus clupeaformis) in the Laurentian Great Lakes have been attributed to a reduction in the amount of zooplankton prey available to young life stages, stemming from the ecosystem effects of invasive dreissenid mussels. Here, we examine the diets of two life stages of lake whitefish, the larval and post-larval stages, in relation to zooplankton availability in the environment at a historically important spawning shoal complex in Lake Huron to better understand the potential for food limitation to influence the growth and survival of these critical early life stages. The digestive tracts of larval (size range 12–26 mm) and post-larval (size range 23–43 mm) lake whitefish were extracted, and contents were identified and enumerated to describe feeding strategies and calculate electivity indices to assess selection for specific prey groups and sizes. We found that the amount of food consumed varied among years and there was an ontogenetic shift in feeding strategy, with larval fish having a more generalist diet than post-larval fish. The most important prey items were calanoid copepods for larvae and copepods and adult/pupa staged dipterans for post-larval fish. Zooplankton densities in the environment were often low, variable among years, and mostly comprised of the smallest zooplankton taxa, nauplii, which were the least preferred prey group of larval fish. The peak in zooplankton density was variable among years, including being absent, and occurred after the peak of larval abundance. Thus, it is possible that low zooplankton availability is increasing the scope for food limitation and contributing to recruitment variation in this population.