Abstract Trace-fossil distribution within the framework of three-dimensional fluvial architecture has been commonly overlooked. The Miocene Vinchina Formation in western Argentina preserves extensive outcrops of fluvial deposits, including architectural elements of both anastomosing and braided systems identified along the Quebrada de La Troya. Multistorey sandy channels, amalgamated sandy channels, heterolithic multistorey channels, channels with gravel bars, abandoned channels, muddy floodplains, crevasse splays, and crevasse channels have been identified. Of these, only the deposits of three elements were bioturbated, namely crevasse splays, anastomosing abandoned channels, and braided abandoned channels. Vertical simple burrows (Skolithos isp.), large-sized J burrows (Capayanichnus vinchinensis), and simple horizontal burrows (Palaeophycus tubularis) are the most common trace fossils in the Vinchina Formation. Other elements include the horizontal meniscate trace Taenidium barretti and the vertebrate footprints Tacheria troyana, Macrauchenichnus troyana, and Ardeipeda isp. The trace-fossil assemblages identified in the Vinchina Formation collectively illustrate the Scoyenia Ichnofacies. In addition, five ichnofabrics are characterized. The position of the water table, substrate consistency, flow energy, and time between depositional events under arid to semi-arid climate conditions were the main parameters controlling bioturbation. Based on detailed observation of the cross-cutting relationship among ichnotaxa, the ichnofabric distribution and the preservation features of the trace fossils studied, a colonization sequence for each of the subenvironments of the Vinchina Formation is proposed in this study. In addition to integration with conventional facies analysis, articulating ichnologic data and fluvial architecture provides further insights into the application of trace fossils to unravel the sedimentary dynamics of alluvial systems.