Zooplankton play an important role as primary consumers in freshwater ecosystems. Many exhibit diel (daily) vertical migration behavior in response to environmental stressors including predation, UV radiation, and anoxia. Horizontal migration, while less thoroughly studied, has been suggested to explain differences between zooplankton density in the water column in the pelagic zone (open water) from day to night. To examine this three-dimensional view of zooplankton migration, we measured both zooplankton and phytoplankton distribution in two lakes in consecutive day/night cycles. These lakes are presumed to have similar levels of zooplanktivory. We did this by sampling both shallow and deep sites and comparing the distributions of primary producers and consumers in different lake zones. We found diel differences in zooplankton density and biomass, as well as a mismatch between zooplankton distribution and phytoplankton distribution, suggesting zooplankton movement is controlled by factors other than proximity to food. We also found differing composition from day to night and by location, consistent with theories of interspecific competition and visual predation. Overall, our results indicate the presence of taxa-specific vertical and horizontal movement, which will directly affect the role of zooplankton connecting trophic levels in freshwater lake food webs.