Major floods elicit calls for more comprehensive and multifaceted approaches to flood management. In the future, adding floodways and flood storage areas to traditional structural strategies (e.g., dams and levees) may be a viable strategy. Beyond reducing flood damages, there is growing societal interest in floodplain services, including nutrient processing and supporting fisheries and wildlife habitat. In April 2013, a record flood on the Illinois River created a natural floodplain management experiment within two restored, but disconnected floodplains. With the benefit of extensive preflood data at both sites, we evaluated the biological response to a minor (levee overtopping) and a major (levee failure) flooding event. Our intent was to test the ecological resilience of restored floodplains to these two alternative management scenarios. We hypothesized that a minor flood event would have little effect on ecosystem structure, whereas the major flood event would result in lower production and diversity of zooplankton, increase invasive vegetation and decrease desirable submerged and emergent aquatic vegetation, and decrease overall waterbird use. Case studies such as this are critically needed to inform policy makers and managers of the trade-offs between alternative floodplain connectivity regimes on ecological services.