Aggregate community-level response to disturbance is a principle concern in ecology because post-disturbance dynamics are integral to the ability of ecosystems to maintain function in an uncertain world. Community-level responses to disturbance can be arrayed along a spectrum ranging from synchronous oscillations where all species rise and fall together, to compensatory dynamics where total biomass remains relatively constant despite fluctuations in the densities of individual species. An important recent insight is that patterns of synchrony and compensation can vary with the timescale of analysis and that spectral time series methods can enable detection of coherent dynamics that would otherwise be obscured by opposing patterns occurring at different scales. Here I show that application of wavelet analysis to experimentally manipulated plankton communities reveals strong synchrony after disturbance. The result is paradoxical because it is well established that these communities contain both disturbance-sensitive and disturbance-tolerant species leading to compensation within functional groups. Theory predicts that compensatory substitution of functionally equivalent species should stabilize ecological communities, yet I found at the whole-community level a large increase in seasonal biomass variation. Resolution of the paradox hinges on patterns of seasonality among species. The compensatory shift in community composition after disturbance resulted in a loss of cold-season dominants, which before disturbance had served to stabilize biomass throughout the year. Species dominating the disturbed community peaked coherently during the warm season, explaining the observed synchrony and increase in seasonal biomass variation. These results suggest that theory relating compensatory dynamics to ecological stability needs to consider not only complementarity in species responses to environmental change, but also seasonal complementarity among disturbance-tolerant and disturbance-sensitive species.