We incorporated faunal datasets from 1950s to 1980s excavations at Modoc Rock Shelter (11R5), a deeply stratified archaeological site in the central Mississippi River valley of southwestern Illinois, into the Digital Archaeological Record (tDAR) as part of a National Science Foundation-funded research project in which nine collaborators in the Eastern Archaic Faunal Working Group (EAFWG) ingested and analyzed faunal datasets from 23 archaeological sites to test hypotheses about changing use of aquatic resources during the Archaic Period (10,000─3000 RCYBP) in the interior Eastern United States. The use of tDAR resulted in the online digital preservation of Modoc Rock Shelter data accumulated by different researchers over five decades from multiple areas of excavation and also provided tools to integrate and synthesize the data. To ensure comparability of Modoc Rock Shelter datasets made by researchers using different coding schemes, we mapped variable attributes to existing and newly created tDAR ontologies. Following the EAFWG taphonomic protocol, we examined evidence for differential bone preservation and destruction caused by weathering, gnawing and chewing, butchering, fragmentation, burning, and bone density-mediated attrition for cultural components of the West Shelter and Main Shelter at Modoc. We also examined potential taphonomic biases caused by differences in recovery techniques, contexts excavated, and settlement function. With due consideration of taphonomic biases, we analyzed variability related to cultural factors and/or environmental change. Using the tDAR integration tool, we compared resource use for the cultural components in the two shelters. Our studies bear out earlier findings that Early Archaic hunter-gatherers at Modoc Rock shelter collected numerous small mammals, especially tree squirrels. Deer hunting and aquatic resource use generally increased during the Middle Archaic; and use of fauna was more specialized in the Late Archaic field camps. We relate these shifts in exploitation to landscape evolution, including stabilization of river systems, development of floodplain lakes, and the opening of the forest in the middle Holocene, as well as to changes in demography and settlement strategies.