Shallow lakes are typically found in one of two stable states, a macrophyte-dominated clear water state or a turbid state due to excessive phytoplankton and suspended sediment. Whether shallow backwater lakes in large river floodplains exhibit similar alternate stable states is less understood. This study considers mechanisms, interactions and feedbacks associated with a shift in environmental conditions and biotic community structure in backwater lakes of a hydrologically dynamic floodplain river system. We use long-term data from backwater lakes to show an increase in submersed aquatic vegetation, improved water quality, and resulting shifts in the community structure of aquatic vegetation and fish following a 4 year period of summer low water discharge on the Upper Mississippi River. Backwater lakes in our study span a gradient of environmental conditions. Backwater lakes located in the upper reach of our study area were chronically turbid and support only sparse aquatic macrophytes, whereas those downriver exhibited clearer water and abundant vegetation. An increase in submersed aquatic vegetation in the lower backwater lakes resulted in a fish community shift to more vegetation-associated species. A lesser response in submersed aquatic vegetation abundance and fish community shift was observed in the upper, more turbid backwater lakes. The combination of vegetative cover and turbidity were key environmental variables associated with fish community structure in lower backwater lakes. Turbidity was the key environmental variable associated with submersed aquatic vegetation in both upper and lower backwaters. Providing further insight into the physical, chemical and biological interactions associated with ecological shifts will help guide management and restoration decisions towards more resilient, macrophyte-rich floodplain backwaters.