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Spatiotemporal patchiness of plankton and appropriate sampling strategy are crucial considerations for long-term studies of plankton dynamics, determining the confidence with which statistically significant ecological changes will be detected and attributed to the drivers. We analyze the spatiotemporal variability of Baltic Sea zooplankton using historical data from various monitoring programs. We determined the scales of highest temporal and spatial variability, focusing on distances and time periods shorter than 100 km and 90 days. Analyses were made for different hydrological regions (small lagoons, larger gulfs, Baltic Proper), and with differently sized zooplankton groups (large and small copepods and cladocerans). Temporal variability in one place usually exceeded the synoptic spatial variability. Smaller, faster reproducing cladocerans varied more in abundance than larger, slower reproducing copepods. The variability increased with time and distance between samples. For copepods, a temporal cycle of 60–70 days emerged, implying the need for sampling after every 20–23 days. For cladocerans, we propose 14 days as a sampling interval, the time during which the average abundance differences between samples doubled. In the future, these guidelines should be used in conjunction or as an addendum to HELCOM (Helsinki Commission) guidelines, to optimize the zooplankton sampling effort in the Baltic Sea.