Northern Appalachian Basin deposits and associated fossils have served as exemplars for ecological-evolutionary investigations, and as the reference interval for the concept of coordinated stasis. Here, we examine faunal and environmental changes within the uppermost Hamilton and lowermost Genesee Groups of the late Middle Devonian succession of New York State. Dramatic diversity loss, faunal migrations, and ecological restructuring recognized in these strata have been used previously to define the end of the Hamilton ecological-evolutionary subunit, and, furthermore, these strata and corresponding faunal changes represent the type region for the global Taghanic Biocrisis. We present and analyze a new, high-resolution data set of post-Taghanic Genesee fossil assemblages, in which we recognize 11 biofacies corresponding to an onshore-offshore (depth) gradient. The Genesee Fauna shows an unexpectedly high taxonomic similarity to nearshore biofacies of the pre-Taghanic Hamilton Fauna, related to the persistence of siliciclastic-dominated nearshore settings through the Taghanic Biocrisis, whereas the onset of anoxic/dysoxic conditions typified offshore portions of the environmental gradient. The “Nearshore Refugium Model” of Erwin offers a possible explanation for the persistence of taxa through the biocrisis in nearshore settings. This constriction was followed by subsequent expansion of these residual taxa to offshore environments in relatively similar associations, as increased Acadian orogenic activity and resultant delta progradation increased habitable space offshore by decreasing the extent of deeper-water, oxygen-poor settings. Although taxonomic similarity was high between the Hamilton and Genesee Faunas, biofacies structure differed primarily because of tectonically driven physical transformations to the basin and associated biotic turnover. Nevertheless, the combination of high taxonomic persistence of Hamilton nearshore taxa and the introduction of relatively few new taxa in the Genesee Fauna resulted in a taxonomic holdover that was much higher than observed in the original formulation of coordinated stasis.