A range of plumbing systems has been identified in deep-water Nigeria by interpreting multi-scale seismic data sets (reprocessed 3D exploration seismic reflection data and 2D very high-resolution near-bottom seismic reflection data) as well as sedimentological and geochemical data obtained from a long sediment core recovered by the seafloor drill rig MARUM-MeBo70. The plumbing systems are characterized by diverse fault networks and lie above tectonic features including thrust/fold structures and strike-slip faults linked to gravity-driven deformation caused by underlying over-pressured shales. The plumbing systems are associated with fluid seeping structures at the seafloor such as pockmarks, mud volcanoes and seafloor zonations colonized by living benthic macrofauna typical of active fluid flow. The comparison of seismic stratigraphic sequences with climate and environmental proxies determined for sediments including lithology, element ratios such as Ca/Fe and Zr/Rb, sedimentation rates, and planktonic foraminifera δ18O records shows a control of short-term (0.1–0.4 Myr) and long-term (around 1 Myr) sedimentary cycles. During short-term fluctuations, the recurrence of fluid seeping structures is controlled by the lithology (coarse-grained versus fine-grained sediments) linked to glacial-interglacial fluctuations and a monsoon regime. Conditions favorable for fluid flow are related to the deposition of coarse-grained layers, glacial periods, sea-level lowstands, and low sedimentation rates. We hypothesize that cyclic gravity-driven sediment deformations controlled by glacial-interglacial and long-term variations in accommodation and sedimentation, have led to the cyclic evolution of the plumbing systems and associated seeping structures since the Plio-Pleistocene.