Population demographics are used by biologists and managers to determine the quality of a fishery and set regulations to achieve desired management goals. Regulating a large river system fishery that spans a substantial geographical region is often complicated by spatially variable environmental factors that affect fish population dynamics (e.g. habitat, water quality); these dynamics are rarely examined within an entire system. In this study we compared spatial differences in population age and length at capture, growth, fecundity and body condition of bluegill Lepomis macrochirus among two different river reaches (e.g. basin width, gradient, velocity) of the Illinois River (Illinois, USA) and a disconnected floodplain lake, the Emiquon Preserve. Variations in selected population demographics were evaluated in relation to well-documented habitat characteristics (e.g. water quality, aquatic vegetation, backwater availability). Differences in bluegill demographic traits between the disconnected floodplain lake and river reaches were distinct, and variations between river reaches were sex specific. The floodplain lake generally had older bluegill that expressed a higher maximum length at age and a lower growth rate and fecundity than bluegill in river reaches. River bluegill differed between river reaches in male growth, and fecundity in both sexes. Body condition was not significantly different among bluegill populations. Early research on floodplain lakes indicates that this habitat supports greater fish growth and higher reproductive fitness than mainstem habitat. We conclude that increasing the availability of quality backwater habitat, even within a highly modified large river system like the Illinois River, could substantially increase the quality and stability of bluegill populations.