The sandstone-shale-coal succession of the Barakar Formation (early Permian) of the Raniganj Basin, India hosts low-diversity ichnoassemblages, containing ichnogenera Arenicolites, Chondrites, Diplocraterion, Monocraterion, Ophiomorpha, Palaeophycus, Planolites, Skolithos, Taenidium, and Thalassinoides, produced by shallow marine infaunal invertebrates. Sedimentary facies architecture depicts a transgressive, fluvio-tidal (with a minor wave) interactive estuarine depositional setting. The fluvial deposits, lying beyond the zone of tidal encroachments, record absence of trace fossils, which is attributed to a low colonization window caused by high fluvial discharge and frequent channel migrations. Tidal interactions with high fluvial discharge led to bay-head deltas in the inner-middle estuary with the dominance of suspension-feeding and deposit-feeding ichnotaxa in coarser- and finer-dominated sediments, respectively, suggesting a mixed Skolithos–Cruziana ichnofacies. Increasing tidal influence with very less fluvial input allowed opportunistic colonizers and deposit feeders of the Cruziana ichnofacies to flourish in the central estuarine setting. Intermittent low-oxygenated restricted conditions marked by the chemosymbiotic ichnoassemblages of the Zoophycos ichnofacies indicate very low energy conditions. The outer estuary with increasing wave dominance is inhabited by suspension-feeding, domicile ichnotaxa of Skolithos ichnofacies, frequently mixed with the ichnotaxa of the Cruziana ichnofacies. The recurrent juxtaposition and lateral distribution of the Seilacherian marginal marine ichnofacies is attributed to complex sediment–organism interaction patterns in response to prevalent energy conditions, sediment discharge and substrate conditions in different zones of the fluvio-tidal estuarine setting. The integrated sedimentological-ichnological model signifies marine transgressions that affected the palaeogeography of the Permian continental Gondwanaland.
$\bullet$ Sedimentological–ichnological analysis signifies marine encroachment in Barakar Formation in peninsular India.
$\bullet$ Ichnoassemblages point to complex pattern of sediment–organism interactions with gross energy distribution.
$\bullet$ Sustained marine transgression event within the continental Gondwanaland during early Permian is visualized.