The effects of reservoir heterogeneity on the development of submarine channel fields are still poorly understood because of lack of direct evidence for fluid flow. This study uses integrated well logs and three-dimensional seismic data from the Niger Delta Basin to characterize the previously undocumented spatial distribution of shale units and permeability contrasts within a submarine channel system. Combining these data with four-dimensional (4-D) seismic data facilitates the exploration of the controls of reservoir heterogeneity on fluid flow during development. The results show that the studied submarine channel system consists of multiple vertically stacked channel complex sets (CCSs) from CCS1 (oldest) to CCS5 (youngest), which are separated from each other by continuous shale barriers. The CCS2–CCS4, which are located in the stratigraphic middle of the channel system, are the main development layers because of their higher permeabilities and lower permeability contrasts. The 4-D seismic responses validate that the presence of shale barriers between vertically adjacent CCSs can hinder the flow of fluids between CCSs. Fluid flow between vertically adjacent CCSs barely occurs except in localized erosional locations where the sand fills of different CCSs are vertically connected. Each CCS consists of multiple individual channels, which can be separated by inclined shale baffles if they laterally migrate in one direction. As the 4-D seismic responses demonstrate, such inclined shale baffles can hinder fluid flow between adjacent individual channels and help to form multiple narrow flow paths in map view. The absence of inclined shale baffles also produces prominent permeability contrasts within each CCS, which are characterized by relatively high–permeability zones that are parallel to the channel axis. Comparison of this permeability distribution and the 4-D seismic responses shows that injected water preferentially sweeps along relatively high–permeability zones, which can help to form single wide flow paths with higher sweep efficiency or single narrow flow paths with lower sweep efficiency.