Water management structures (WMS) are used to regulate water levels between large floodplain river backwaters and their adjacent river systems offering a balance between maintaining quality backwater habitat and providing benefits to the river systems. The design and operation of these WMS is dependent on unique management goals, and their impacts on the surrounding ecosystem are understudied. From 2016–2018 we quantified the response of the surrounding fish assemblages (i.e., backwater and river abundance and composition) to the WMS operation at the Emiquon Preserve, a 2723 ha restored floodplain lake located adjacent to the main channel of the Illinois River, U.S.A. Environmental conditions were recorded, and fish were collected using boat electrofishing on both sides of the WMS under three operational levels: closed and no flow, gravity flowing water, and mechanically pumping water to the river. Multivariate analyses determined that there was no difference in fish community composition within the Emiquon Preserve among operation levels. Within the river there were differences in community composition when the WMS was closed and mechanically pumping water. Environmental parameters varied seasonally and WMS operation level varied but indicated an increase in chlorophyll-a in the river when the WMS was mechanically pumping water, although the chlorophyll-a decreased within 200 m downstream of the WMS in the Illinois River. This study suggests that managed connections between restored backwater and habitats operated like this WMS have variable, spatially isolated impacts on fish communities despite supplying chlorophyll-a to large river ecosystems.