This paper documents a subsurface trace fossil and ichnofabric study of the proximal parts of a structurally confined and channelized sand-rich, lower slope and proximal basin-floor deep-marine system in the Middle Eocene Ainsa basin, Spanish Pyrenees. Five depositional environments are recognized based on sedimentary facies associations, depositional architecture and stratigraphic context (channel axis, channel off-axis, channel margin, leveé-overbank and interfan), as well as a channel abandonment phase. Each environment is characterized by distinct and recurring ichnofabrics. Ichnological measurements and observations were recorded from six cores recovered from six wells drilled at a spacing of between 400 m and 500 m at outcrop, and totalling 1213 m in length. From channel axis to levée-overbank environments, there is a trend of increasing bioturbation intensity and ichnodiversity. Ichnofabrics in channel axis and channel off-axis environments are characterized by low bioturbation intensity and low ichnodiversity. Thalassinoides-dominated firmground ichnofabrics associated with erosive sediment gravity flows are common in these environments. In contrast, channel margin and levée-overbank environments are characterized by ichnofabrics associated with high bioturbation intensity and ichnodiversity. Sediments of the interfan are characterized by the highest bioturbation intensity, associated with burrow mottling and an absence of primary sedimentary structures. This paper demonstrates that in core-based studies, ichnofabric analysis is an important and valuable tool in discriminating between different environments in channelized deep-marine siliciclastic systems. The results of this study should find wide applicability in reservoir characterization studies in the petroleum industry, in field-based analogue ichnofabric studies and other core-based studies in deep-water siliciclastic systems worldwide such as the Integrated Ocean Drilling Program.