In this paper we test the usefulness of acoustic backscatter measurements from a 614 kHz Acoustic Doppler Current Profiler (ADCP) for the qualitative and quantitative characterisation of zooplankton distributions in lakes. ADCP-based backscatter estimates were compared with frequent net hauls obtained during a calibration experiment in which the acoustic backscatter was strongly dominated by vertical migrating Chaoborus flavicans larvae.2. The correlation between backscatter estimates and the C. flavicans concentration was very good. Vertical swimming speed of larvae, measured directly by the ADCP, was up to a maximum of 5 mm s−1 and agreed very well with the observed vertical movement of the backscatter contour lines. Although the strong backscatter from C. flavicans overwhelmed the signal from the remaining zooplankton, a good correlation between backscatter strength and the total remaining zooplankton concentration, dominated by Cyclops spp., was found for the depth and time intervals where no C. flavicans were present.3. In addition to the calibration experiment, longer-term ADCP measurements from different lakes revealed a strong temporal correlation between the onset of the up- and downward migration of zooplankton and the local sunset and sunrise.4. We conclude that ADCPs can be used to monitor plankton distributions both temporally and spatially. It also seems possible to estimate plankton densities after appropriate calibration.