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1. We present data with a high spatio-temporal resolution from a 72-h field survey in Bautzen Reservoir (Saxony, Germany). The aims of this survey were to observe hydrophysical processes during a period of unstable stratification in spring and investigate the effect of wind-induced internal waves on the vertical distribution of zooplankton. 2. Wind velocities up to 10 m s−1 caused a strong downwelling event of warm water at the sampling site and led to the generation of internal waves with an amplitude of 4 m. 3. The zooplankton community, which was dominated by Daphnia galeata, inhabited epilimnetic waters. Downwelling enlarged the thickness of the epilimnetic layer and, hence, led to high zooplankton abundances down to relatively deep water strata indicating lateral transport of zooplankton. As a consequence, area-specific zooplankton abundances increased considerably (max. fourfold) during downwelling. 4. We conclude that classical limnological field sampling, such as for monitoring purposes, can lead to severely biased estimates of zooplankton abundance due to the interfering effects of hydrophysical processes like internal waves. 5. Backscattering strengths measured by a simultaneously deployed Acoustic Doppler Current Profiler (600 kHz) were found to be correlated with estimated zooplankton abundances based on plankton samples. [ABSTRACT FROM AUTHOR]