Here we investigate the diel vertical migration (DVM) of the different larval stages of Chaoborus flavicans between spring and summer in two different lakes and three different years. Specific attention is given to the influence of the vertical distribution of dissolved oxygen (DO) on the DVM of the different larval instars. To our knowledge, this study is the first that combines continuous observations of DVM of C. flavicans with continuous measurements of DO distributions over several months, allowing the assessment of changes in DVM due to the development of hyperoxic conditions in the deep water of lakes. With ontogenetic development, C. flavicans larvae increase their sensitivity to changes in light intensity and their tolerance to low oxygen conditions. Our results suggest that the physiological changes of C. flavicans larvae are adaptations to seasonal changes in DO, improving migration abilities to enable utilization of hypoxic and anoxic waters to avoid predation. Interannual change in the abundance and vertical distribution of phytoplankton affecting DO concentrations was sufficient to alter DVM patterns of C. flavicans larvae between years.