Floodplain lakes of large river systems contain fish habitats that are not found elsewhere within the river, and these lakes have a diversity of environmental conditions that vary in space and time. Our objective was to examine relationships between floodplain lake fish communities and environmental variables associated with lake morphology, water chemistry, and river‐floodplain connectivity in a large river‐floodplain ecosystem. Multivariate direct‐gradient analyses indicated that lake surface area, lake depth, water clarity, and (to a lesser extent) dissolved oxygen were the most important factors in the structuring of lake fish communities. Results further suggested that floodplain lakes could be placed into groups that contained distinctive fish communities. Fish community structure was not strongly related to river‐floodplain connectivity, though fish species richness in individual lakes was positively correlated with degree of flooding in those lakes. Fish species diversity in lakes was positively correlated with linear distance between lakes and the main river channel; lakes that were furthest from the main river channel had more diverse fish communities. The diversity of environmental conditions in floodplain lakes is essential for maintaining net ecosystem diversity in large river ecosystems.