To understand how aquatic macroinvertebrate assemblages vary among side channels across a large floodplain river ecosystem, we collected macroinvertebrates from 23 side channels distributed across six reaches of the Upper Mississippi River and Illinois River and quantified taxonomic and functional indices. Within this data release, three products are included: 1) site-level environmental data, 2) raw assemblage data and derived taxonomic and functional indices, and 3) species functional traits.