Many shallow lakes have lost a large part of their ecological value during the past decades. Human-induced factors such as eutrophication and inappropriate fish stock management are generally the main causes for this loss. To restore such degraded habitats, several measures are taken, typically involving a reduction of nutrient loading and interventions in the aquatic food web functioning (biomanipulation). In this study, we report on the joint effects of a series of restoration measures in a shallow lake (Lake Kraenepoel, Belgium, 22 ha) and evaluate these effects via three different criteria. The first criterion is that the target condition, being a clearwater phase with submerged macrophytes, was successfully achieved and persisted for a period of at least 5 years after restoration. Second, we detected a substantial change in community structure of cladoceran zooplankton and an associated increase in species richness and conservation value following restoration measures. Finally, we observed that the general structure of the present day cladoceran zooplankton community resembles well that of the preeutrophication period (1929-1931). Current species richness, however, tends to be lower than in the reference period, and some rare species are still lacking. It is conceivable that, when submerged macrophytes develop further, a subset of specialist species may reappear. Overall, the use of historical habitat-specific samples offers a major opportunity for evaluating restoration success in great detail. Community structures may directly be compared, the gain or loss of specific species can accurately be documented, and more insights in the observed patterns be obtained.