This dataset includes information from multiple taxa collected from four main reaches in the Upper Mississippi River Basin, including La Grange reach of Illinois River, Pool 2 of Mississippi River, Pool 19 of Mississippi River, and the St. Croix River. Taxa include hydropsychid caddisflies, chironomids, hexagenia mayflies, threeridge mussels, mapleleaf mussels, Wabash pigtoe mussels, bigmouth buffalo, gizzard shad, and bluegill. Seston samples were also collected, in addition to water samples for identifying and enumerating phytoplankton species. Fatty acids, lipids, and stable isotopes were quantified for the aforementioned taxa. Water quality data were recorded at the time of sample collection and discharge data was obtained from US Geological Survey and the US Army Corps of Engineers. Six worksheets are included in this file, including a meta-data sheet that describes the datasets, provides variable names, and associated units of measure.