Community biomass is often less variable than the biomasses of populations within the community, yet attempts to implicate compensatory dynamics between populations as a cause of this relationship often fail. In part, this may be due to the lack of appropriate metrics for variability, but there is also great potential for large‐scale processes such as seasonality or longer‐term environmental change to obscure important dynamics at other temporal scales. In this study, we apply a scale‐resolving method to long‐term plankton data, to identify the specific temporal scales at which community‐level variability is influenced by synchrony or compensatory dynamics at the population level. We show that variability at both the population and community level is influenced strongly by a few distinct temporal scales: in phytoplankton, ciliate, rotifer, and crustacean communities, synchronous dynamics are predominant at most temporal scales. However, in phytoplankton and crustacean communities, compensatory dynamics occur at a sub‐annual scale (and at the annual scale in crustaceans) leading to substantial reductions in community‐level variability. Aggregate measures of population and community variability do not detect compensatory dynamics in these communities; thus, resolving their scale dependence unmasks dynamics that are important for community stability in this system. The methods and results presented herein will ultimately lead to a better understanding of how stability is achieved in communities.