The upper Paleogene strata of the U.S. Gulf Coastal Plain host a rich and widely celebrated record of marine macroinvertebrate fossils, which are vital to Cenozoic paleontology. However, their regional correlation and depositional evolution have long been controversial, owing to their limited outcrop exposure and complex regional facies relations. This has consequently inhibited detailed paleoecological study, particularly regarding any putative temporal and/or environmental trends in paleocommunity structure. Here, I propose a new depositional model for the upper Claiborne, Jackson, and Vicksburg groups of Mississippi, which emphasizes the spatiotemporal relationship between updip, deltaic siliciclastics exposed in outcrop and the downdip carbonate factory known primarily from subsurface study. This framework provides a basis for refined stratigraphic interpretation and paleoecological analysis within the context of an evolving, mixed carbonate-siliciclastic margin. Using a synthesis of biostratigraphic range data, field relations, and subsurface observations, I provide a new correlation framework for the middle Eocene Kosciusko and Cook Mountain formations of Mississippi and the upper part of the Lisbon Formation of Alabama (Claiborne Group). This hypothesis demonstrates the governing effects of expressed depositional environments on observed taxonomic range data and permits a new approach to paleocommunity study for this interval through the analysis of biofacies relative to an evolving gradient of siliciclastic and carbonate environments. A suite of multivariate statistical techniques is applied to assemblage data to codify biofacies, relate them to their underlying environmental factors, and test for faunal differences through a temporal shift from nearshore deltaic/muddy ramp deposition to offshore carbonate shelf deposition. This environmental change through time drives a strong, statistically significant shift in paleocommunity composition, documented in both taxonomic and guild abundance data. Faunal turnover through repeated packages of siliciclastic and carbonate strata therefore reflects, in part, the varying expression of biofacies related to shore position and carbonate production. Further comparison of these assemblages to other Gulf Coast faunas suggests the persistence of similar gradients and the repeated expression of comparable biofacies throughout the upper Paleogene, facilitating further paleobiological studies in this setting.