Temporal variability of vertical zooplankton distributions is analyzed on timescales from minutes to days based on 7 months of acoustic backscatter strength data in Lake Constance. A comparison with net samples reveals that most of the observed variability in volume backscatter strength is associated with variations in the abundance of large Daphnia. Diel vertical migration (DVM) of zooplankton was a persistent feature throughout the entire period of observation, while amplitude, daily migration timing, and migration speed varied with season. This active motion of zooplankton was affected by internal waves on a broad range of timescales. In spring, the maximum depth of DVM follows variations in isothermal depths associated with long-wavelength, basin-scale internal waves. Propagating, short-wavelength, internal waves with comparable amplitudes affect vertical zooplankton distributions on timescales of minutes. Spectral analyses of zooplankton abundance, temperature, and current velocity reveal close correspondence of spectral peaks and slopes, indicating that up to timescales of several days, the only temporal scale at which biological processes dominate over passive transport is associated with DVM. Whereas horizontal transport dominates at long periods, vertical transport occurs only at short timescales.