Community assembly following disturbance is a key process in determining the composition and function of the future community. However, replicated studies of community assembly at whole-ecosystem scales are rare. Here, we describe a series of whole-lake experiments, in which the recovery of zooplankton communities was tracked following an ecosystem-scale disturbance, that is, application of the piscicide, rotenone. Using a before-after-control-impact design, 14 lakes in eastern Washington were studied: Seven lakes were treated with rotenone, while seven lakes acted as reference systems. Each lake was monitored up to 6 months before and 1–2 years after the rotenone treatments. Zooplankton samples and environmental measurements were collected approximately monthly from each lake. Community responses following disturbance were assessed using metrics of abundance, diversity, and community composition, as well as taxonomic group abundance. Zooplankton recovery was also assessed using species traits related to habitat, feeding mode, trophic level, body size, and life history. In addition to patterns of recovery, potential mechanisms were explored relating to abiotic conditions, biotic interactions, and traits. There were steep declines in the abundance (average across years: 99%) and diversity (average across years: 75%) of the zooplankton community following rotenone treatment. Although abundance had recovered by the second year of the study, community diversity had not fully recovered after 2 years. Communities from rotenone lakes appeared to be compositionally recovered within about 8 months following disturbance. Cyclopoid copepods were typically the first group to recover and remained dominant for a few months, whereas cladocerans recovered more slowly, typically within ~6–7 months following rotenone. Calanoid copepods were not fully recovered 2 years after rotenone treatment. Traits related to body size and feeding mode were associated with the zooplankton communities following rotenone treatment. We failed to observe significant spatial synchrony in recovery patterns of zooplankton across lakes, though we did observe significant synchrony of zooplankton taxonomic groups within lakes. These findings suggest that traits related to ecological function, and to a lesser extent, biotic, and abiotic factors, as well as characteristics of the disturbance itself, may be important in helping to understand recovery processes