This is a case study of the Lake Michigan ecosystem. The basic goal of the research program has been to improve understanding of food web relations, productivity and recruitment processes through the investigation of large-scale natural perturbations. Recent invasion of the laurentian Great Lakes by a predatory invertebrate never before present in the Nearctic has altered ecosystem food webs at a middle trophic level. Changes have subsequently occurred in zooplankton species composition, and in recruitment success of some fish species. These changes may be linked. The arrival of the invading predator in Lake Michigan has been documented, the first food web changes have been quantified, and the background, baseline conditions against which changes can be judged have been established. The results from Lake Michigan prompted a new examination of historical data from Lake Washington, one of the most important analog studies, and yielded the discovery that nutrients produce distinctly different results at the ecosystem level than do food web changes. %%% The structure of the food web of Lake Michigan has changed substantially since the introduction of the predators Bythotrephes and Leptodora. The lake was under study before the predators arrived, and continued examination of its food chain dynamics and community structure will provide important insight on the adjustment of aquatic ecosystems to major perturbations in their food webs. The contained nature of the Great Lake ecosystem makes it an ideal site for such an investigation.