Dike structures, designed and installed by the U.S. Army Corps of Engineers in the Lower Mississippi River, can modify river geomorphology, discharge rates, and sediment movements within the river. These changes in the river's characteristics, plus the presence of the dikes themselves, result in shifts in types, sizes, and variety of aquatic habitats on a yearly basis. At low water river stages, isolated dike pools bordered by bars are formed, creating distinct aquatic habitats which are quite variable in size and depth. Fish and water samples collected in two such dike pools as well as from the adjacent river border wee used to determine the importance of dike pool habitats to fish communities during a low water period of 1980. Hydrological results indicate that overall differences in water quality were easily distinguishable once stratification began. Surface readings of dissolved oxygen, temperature, and pH were generally higher in the pool habitats than in the main channel. As depth increased, the opposite was true for dissolved oxygen, temperature, and pH. Conductivity at the bottom in the pools during isolation was much higher than in the main channel.

Variation in community composition (presence/absence data) and structure (relative abundance) of Upper Mississippi River fishes was assessed using data from the Long Term Resource Monitoring Program collected from 1994 to 2002. Community composition of fishes varied more in space than through time. We found substantial variation in community composition across two spatial scales: large-scale differences between upper and lower river reaches and small-scale differences among individual regional trend areas (RTA). Community structure (relative abundance data) of fishes also varied more through space than through time. We found substantial variation in fish community structure at three spatial scales: (1) large-scale differences between upper and lower river reaches, (2) differences among individual RTA, and (3) differences among habitat strata, with backwaters having a distinct community structure relative to the main channel and side channels. When averaged across all RTA, fish community structure in 1994 and 1995 was distinct from all other years, possibly as a result of the 1993 Flood. Fish community structure observations for each RTA and year correlated with the environmental variables measured at each sample site. A canonical approach revealed that the combination of Secchi depth, water temperature, current velocity, and vegetation abundance had the greatest correlation with community structure.