An integrated analysis of ichnological and sedimentological features in ancient successions provides a robust dataset of high-resolution interpretations of environmental parameters, encompassing both depositional and ecological aspects. By characterising discrete and recurring bioturbation patterns in the Puerto Madryn Formation (Late Miocene, Argentine Patagonia), we arrive at key knowledge about predominant environmental stresses within transgressive phase shallow marine and estuarine systems, shedding light on their palaeoenvironmental implications. Given the inherent complexities of coastal settings, including the challenges posed by omission/erosion surfaces, it becomes imperative to consider the intricate interplay of multiple depositional processes and environmental factors.Through a detailed integration of sedimentological and ichnological approaches, we discern the establishment of a wave-dominated system overlain by a tide-dominated estuarine system.The wave-dominated marine system involves tabular bodies extending laterally over tens of kilometres, with upward fining and coarsening successions from the mid- to lower-shoreface to offshore-shelf environments. The influence of waves and tides on these systems is discussed in the absence of physical sedimentary structures and the need to find elements that bring us closer to elucidating whether waves or tidal processes influence shoreface to offshore systems. The ichnological assemblages allow for the characterisation of Cruziana ichnofacies with proximal (Taenidium and Thalassinoides), archetypal (Asterosoma, Chondrites, Cylindrichnus, Ophiomorpha, ?Rhizocorallium, Rosselia, Scolicia, Sinusichnus, Siphonichnus, Teichichnus, and Thalassinoides), and distal expressions (Chondrites, Helicodromites, Phycodes, Thalassinoides, and ?Zoophycos) in the lower shoreface to lower offshore and transitional settings with the shelf. However, the transition from these deposits to Chondrites-dominated beds associated with lower offshore to shelf environments—determined by changes in oxygenation, nutrients, and energy conditions—impedes assignment of all the successions to a particular ichnofacies.The tide-dominated estuarine system features wide, channel-shaped bodies filled with sandy to heterolithic facies, interpreted as intertidal and subtidal deposits. To differentiate between estuary mouths and other settings, the analysis involved characterisation of transgressive and regressive surfaces, ichnological assemblages, and facies distribution, determining net sediment movement—whether landwards or seawards—and its influence on system classification. The ichnological assemblages could be assigned to the Skolithos (Arenicolites, Gyrolithes, Maiakarichnus, Ophiomorpha, Schaubcylindrichnus, Skolithos, and Thalassinoides) and Cruziana ichnofacies (Ophiomorpha, Rosselia, Scolicia, and Siphonichnus). Variations in diversity and abundance often help to determine certain stressful conditions, although the transition to more open areas is discussed, addressing how it could modify the typical models linked with a direct relationship between abundance/diversity and physico-chemical stress.