We sampled macroinvertebrate assemblages in the littoral benthos and on the surface of snags in the Upper Mississippi, Missouri, and Ohio rivers. Snag assemblages differed from benthic assemblages. Tubificids, Caenis, Tanytarsus, Cryptochironomus, Limnodrilus, and Chironomini were consistently more abundant in the benthos; Nais, Cricotopus/Orthocladius, Nematoda, and Rheotanytarsus were consistently more abundant on snags. Filterers were more abundant and gatherers were less abundant on snags than in the benthos. Snag assemblages differed among rivers and among reaches within rivers. Variation among reaches was the result of direct and indirect effects of high-dam reservoir impoundments (upper vs lower Missouri River) and low-dam impoundment for navigation (impounded vs free-flowing Upper Mississippi River). The maximum relative abundance of filterers in the lower Missouri River, which was the only long unregulated reach we studied, was related to particulate organic C and sestonic chlorophyll a concentration, which increased with distance downriver from the lowest main-stem dam. Snag diameter, snag-surface characteristics, and water depth did not affect the composition of snag assemblages, but the dominant taxa on snags in fast-velocity locations were different from the dominant taxa on snags in slow-velocity locations. Relatively few taxa showed strong longitudinal patterns in relative abundance within a reach, and only on the Missouri River. We hypothesize that the many navigation dams on the Ohio and Upper Mississippi rivers suppress the development of environmental gradients and inhibit the formation of longitudinal patterns in macroinvertebrate assemblages. Snag assemblages were dominated by a few taxa (genus-level and higher), a characteristic that might constrain the sensitivity of the assemblages to some human impacts. Sampling snag assemblages has potential for great-river bioassessment, but further research is necessary on sampling methods and sensitivity of assemblages to stressors.