The Mississippi Alluvial Valley between southern Illinois and southern Louisiana contains hundreds of floodplain lakes, most of which have been adversely affected by landscape modifications used to control flooding and support agriculture. We examined fish assemblages in lakes of this region to determine whether deterministic patterns developed in relation to prominent abiotic lake characteristics and to explore whether relevant abiotic factors could be linked to specific assemblage structuring mechanisms. The distributions of 14 taxa in 29 lakes were governed primarily by two gradients that contrasted assemblages in terms of lake area, lake elongation, and water clarity. The knowledge of whether a lake was clear or turbid, large or small, and long or short helped determine fish assemblage characteristics. Abiotic factors influenced fish assemblage structures, plausibly through limitations on foraging and physiological tolerances. Determinism in assemblage organization of floodplain lakes relative to recurrence in physicochemical features has been documented for unaltered rivers. Whereas the Mississippi Alluvial Valley has been subjected to vast anthropogenic disturbances and is not a fully functional floodplain river, fish assemblages in its floodplain lakes remain deterministic and organized by the underlying factors that also dictate assemblages in unaltered rivers. In advanced stages of lake aging, fish assemblages in these lakes are expected to largely include species that thrive in turbid, shallow systems with few predators and low oxygen concentrations. The observed patterns related to physical characteristics of these lakes suggest three general conservation foci, including (1) watershed management to control erosion, (2) removal of sediments or increases in water level to alleviate depth reductions and derived detriments to water physicochemistry, and (3) management of fish populations through stockings, removals, and harvest regulations.