Abstract Sedimentation in the Nuayyim Formation across subsurface central and eastern Saudi Arabia has been chiefly ascribed to continental sedimentary environments. However, a number of levels in this formation show evidence for marginal-marine and shallow-marine sedimentation. This paper documents trace-fossil faunas and sedimentological characteristics from these facies and presents a regional depositional model for the Wudayhi Member that confirms the presence of shallow-marine sedimentary environments. Marginal-marine and shallow-marine sedimentation in the Wudayhi Member includes estuarine deposits and upper-shoreface through lower-shoreface deposits. They are reflective of several transgressive–regressive (T-R) cycles in an overall shoaling-upwards, tidally influenced progradational succession that exhibit mixed-process (wave-, tide-, and fluvially-influenced) depositional environments. The succession displays an overall upward decrease in bioturbation intensity with elements of an impoverished proximal expression of the Cruziana Ichnofacies at the base in proximal- and distal- lower-shoreface deposits (Facies 5–6), passing into an impoverished expression of the Skolithos Ichnofacies in upper-shoreface deposits (Facies 4). Therein, Facies 5 records storm-influenced sedimentation and includes hummocky cross-stratification (HCS), combined-flow ripples, cross-lamination, and ichnofossils that alternate between storm-related and fair-weather assemblages. An overall reduction in both the diversity of ichnogenera and the intensity of burrowing across the shoreface profile, an apparent lack of middle-shoreface deposits, and the occurrence of storm-wave-generated structures interspersed with tidally generated structures in the center and southeast of the study area are interpreted as tidal modulation, suggesting macrotidal conditions at the time of sediment deposition. Estuarine sedimentation includes coal deposits (Facies 1), tidal flats (Facies 2), and fluvio-tidal deposits (Facies 3) that overlie the succession, and display a stressed, impoverished mixture of traces with facies-crossing elements of the Skolithos and Cruziana Ichnofacies in the north and northwest of the study area. Sedimentation took place on a broad and sandy, partially restricted shelf, chiefly influenced by tidal currents that was variably fluvially influenced. The interplay of the aforementioned processes results in a complex architecture that is traceable, based on the sedimentological and ichnological content. Colonization by bioturbating infauna exhibiting elements of an overall impoverished Skolithos and Cruziana Ichnofacies in the Wudayhi Member is interpreted to be related to sea-level rise, with regional transgression induced by the melting of glacier ice following the Late Carboniferous to Early Permian glaciation that affected southern Gondwana. Subsequently, as the Arabian Plate migrated northwards, isostatic rebound concomitant with increased tectonism associated with the Neotethys propagating into the Arabian Peninsula caused regional regression responsible for the progradational sequence presented herein in the Early to Middle Permian. Trace-fossil associations and ichnofacies presented in this paper are significant, because they provide evidence for marginal-marine and shallow-marine tide- and storm-influenced processes in the Unayzah Group during deposition of the Wudayhi Member of the Nuayyim Formation. Furthermore, it establishes a framework than can be linked to fully marine coeval deposits southeastern of the Arabian Peninsula into Oman.