We provide evidence that internal waves cause frequent vertical migrations (FVM) in fishes. Acoustic data from the Benguela Current revealed that pelagic scattering layers of fish below ~140 m moved in opposite phases to internal waves, ascending ~20 m towards the wave trough and descending from the wave crest. At the trough, the downward displacement of upper waters and the upward migration of fish created an overlapping zone. Near-bottom fish correspondingly left the benthic boundary zone at the wave trough, ascending into an acoustic scattering layer likely consisting of zooplankton and then descending to the benthic boundary zone at the wave crest. We suggest that this vertical fish migration is a response to fluctuations in light intensity of 3 to 4 orders of magnitude caused by shading from a turbid surface layer that had chlorophyll a values of 3 to 4 mg m−3 and varied in thickness from ~15 to 50 m at a temporal scale corresponding to the internal wave period (30 min). This migration frequency thus is much higher than that of the common and widespread light-associated diel vertical migration. Vertical movements affect prey encounters, growth, and survival. We hypothesize that FVM increase the likelihood of prey encounters and the time for safe visual foraging among planktivorous fish, thereby contributing to efficient trophic transfer in major upwelling areas.