Lay AbstractWind‐driven internal gravity waves, oscillations of a fluid density surface, are a common feature within the strongly stratified thermocline region of mid‐latitude lakes. We demonstrate that internal waves can propagate within the surface waters, or epilimnion, of Lake Opeongo, Ontario, during periods of weak stratification. We also note that within the epilimnion, zooplankton are not uniformly distributed spatially but are often distributed in patches as a result of the combination of their own movements and the effect of water currents. Using field data from July and August 2009 and 2010 we report observations of the relationship between enhanced heterogeneity of distribution in zooplankton and the presence of internal waves in the epilimnion. To quantify this relationship we compare measurements of small‐scale spatial distributions of zooplankton with a measure of wave activity. For the smallest size ranges of zooplankton (284–450 μm) we find that spatial variability is statistically greatest when internal waves are most active, whereas no such relationship exists for the two larger zooplankton size classes. The vertical velocities associated with the movement of internal waves are estimated to be faster than the swimming speeds of small zooplankton, essentially rendering them passive. This supports our assertion that the movement of internal waves contributes to the increased spatial variability of zooplankton in lakes.