Macroinvertebrate community structure was compared between habitat types within a navigation pool and between navigation pools of the Upper Mississippi River. Bottom samples were taken using a grab or Wilding sampler from 40 and 14 stations on Pool 19 and 26, respectively. In both Pools, distinct communities developed based on substrate type or the presence of aquatic macrophytes rather than specific habitats as defined by river morphometry. Areas with sand substrates usually had communities of low density and diversity. Communities of the highest density, including Hexagenia or Musculium or both, occurred in habitats with silt-sand substrates. However, these areas were low in diversity. High diversity was found in both vegetated areas and habitats with coarse substrates, the latter dominated by net-spinning caddisfly larvae. Due to pool age and longitudinal distribution of species, community similarity between Pools 19 and 26 was not significant, p < 0.05, but functional feeding similarities occurred between communities from the same type of substrate.