The Yazoo River Basin of Mississippi includes several rivers and hundreds of floodplain lakes within an area greatly impacted by agriculture. I studied 17 of these lakes distributed over the lower half of the Yazoo River Basin to document fish assemblages and limnological patterns and to identify environmental variables that might influence these assemblages. Potential connectivity of the lake to parent river and wetland-lake area ratio in the watershed were related to the limnological conditions and fish communities. Lakes with greater potential connectivity tended to be deeper and had greater specific conductance and greater fish species richness including more riverine species. Conversely, as the potential connectivity decreased, lakes were shallower, had greater chlorophyll-a fluorescence, wetland-lake area ratio, and a less speciose lacustrine fish community. Species richness and assemblage composition of riverine species were related directly to potential connectivity. Lacustrine species assemblages were linked to wetland-lake area ratio and turbidity.