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Habitat and hydrology indices were developed to assess the conditions in reaches of the impounded Mississippi river, the Fort Peck and Garrison reaches of the upper Missouri river, the Missouri National Recreational river (MNRR), the channelized lower Missouri river, and the Ohio river. Data were obtained from field sampling, air photo interpretation, and U.S. Geological Survey (USGS) hydrologic records. Habitat and hydrology attributes were incorporated into four habitat indices (channel complexity, substrate quality, littoral cover, and riparian condition) and one hydrology index. Construction of habitat indices for these very large rivers was complicated by a lack of previous research demonstrating methods for choosing and weighting the metrics used to compose these indices. Many habitat metrics used to assess habitat quality in small rivers proved irrelevant or impractical for assessing habitat quality in the upper Mississippi, Missouri, and Ohio rivers. In addition, these very large rivers, unlike smaller streams, were subject to physical and hydrological alterations due to channelization, revetment, levees, and dams. Because of the lack of proven indicators of habitat condition in very large rivers, we began with a large number of measures of natural and anthropogenic stress, eliminating only those metrics that failed tests of range, redundancy, and correlation with longitudinal position along the river. The lock and low-head dam sequences on the impounded Mississippi and Ohio influenced both hydrological patterns and the resident fish community, with conditions recovering with increased distance below dams, until hydrology was once again altered by impoundment from a downriver dam. Channel complexity and hydrology indices displayed the highest correlations with a multimetric fish index, possibly because these indices integrated habitat condition over a larger scale than the transect- and site-scaled littoral cover and riparian indices. Data limitations prevented the calculation of a littoral cover and a channel complexity index for the upper Missouri and Ohio rivers, respectively. Published by Elsevier Ltd.