We investigated the distribution of benthic macroinvertebrates in four aquatic habitat types in the lower Mississippi River: dike fields, a natural bank, a secondary channel, and an abandoned channel over a high flow (flood stage), two moderate, and two low flow periods. The biotas present in the natural bank, the secondary channel, and the abandoned channel showed only minor changes in composition over the various flow regimes. The natural bank was consistently dominated by the burrowing mayfliesTortopus incertusandPentagenia vittigeraand hydropsychid caddisflies; the consistently most common taxa in the secondary channel were the sand-dwelling chironomidsRobackia clavigerandChernovskiia orbicus; phantom midges, tubificid oligochaetes, and fingernail clams were always the most abundant macroinvertebrates in the abandoned channel. The dike fields, however, showed large changes in biotic composition over the different flow regimes. These compositional changes correlated with changes in river stage and resultant alterations in current and substrate. This study indicates that the distribution of macroinvertebrates in the lower Mississippi River is a function of the physical characteristics of the system, notably current velocity and substrate composition.