Diel vertical migrations are common among many aquatic species and are often associated with changing light levels. The underlying mechanisms are generally attributed to optimizing foraging efficiency or growth rates and avoiding predation risk (μ). The objectives of this study were to (1) assess seasonal and interannual changes in vertical migration patterns of three trophic levels in the Lake Superior pelagic food web and (2) examine the mechanisms underlying the observed variability by using models of foraging, growth, and μ. Our results suggest that the opossum shrimp Mysis diluviana, kiyi Coregonus kiyi, and siscowet lake trout Salvelinus namaycush migrate concurrently during each season, but spring migrations are less extensive than summer and fall migrations. In comparison with M. diluviana, kiyis, and siscowets, the migrations by ciscoes C. artedi were not as deep in the water column during the day, regardless of season. Foraging potential and μ probably drive the movement patterns of M. diluviana, while our modeling results indicate that movements by kiyis and ciscoes are related to foraging opportunity and growth potential and receive a lesser influence from μ. The siscowet is an abundant apex predator in the pelagia of Lake Superior and probably undertakes vertical migrations in the water column to optimize foraging efficiency and growth. The concurrent vertical movement patterns of most species are likely to facilitate nutrient transport in this exceedingly oligotrophic ecosystem, and they demonstrate strong linkages between predators and prey. Fishery management strategies should use an ecosystem approach and should consider how altering the densities of long-lived top predators produces cascading effects on the nutrient cycling and energy flow in lower trophic levels.