Process-physics-based, coupled hydrodynamic–morphodynamic delta models are constructed to understand preserved facies heterogeneities that can influence subsurface fluid flow. Two deltaic systems are compared that differ only in the presence of waves: one river dominated and the other strongly influenced by longshore currents. To understand an entire preserved deltaic succession, the growth of multiple laterally adjacent delta lobes is modeled to define delta axial to marginal facies trends through an entire regressive–transgressive depositional succession. The goal is to refine a facies model for symmetrical wave-dominated deltas (where littoral drift diverges from the delta lobe apex). Because many factors change depositional processes on deltas, the description of the river-dominated example is included to provide a direct reference case from which to define the impact of waves on preserved facies patterns. Both systems display strong facies trends from delta axis to margin that continued into inter-deltaic areas. River-dominated delta regression preserved a dendritic branching of compensationally stacked bodies. Transgression, initiated by sea-level rise, backfilled the main channel and deposited levees and splays on the submerging delta top. Wave-dominated deltas developed dual clinoforms: a shoreface clinoform built as littoral drift carried sediment away from the river month and onshore, and a subaqueous delta-front clinoform composed of sediment accumulated below wave base. Although littoral drift in both directions away from the delta axis stabilized the position of the river at the shoreline, distributary-channel avulsions and lateral migration of river flows across the subaqueous delta top produced heterogeneities in both sets of clinoform deposits. Separation of shoreface and subaqueous delta-front clinoforms across a subaqueous delta top eroded to wave base produced a discontinuity in progradational vertical successions that appeared gradual in some locations but abrupt in others. Littoral drift flows away from adjacent deltas converged in inter-deltaic areas, producing shallow water longshore bars cut by wave-return-flow channels with associated terminal mouth bars. Transgression initiated by sea-level rise initially led to vertical aggradation of wave-reworked sheet sands on the subaqueous delta top and then retreating shoreface barrier sands as the subaerial delta top flooded. Pseudo inter-well flow tests responded to local heterogeneities in the preserved deposits. As expected, abandoned channels in the river-dominated case defined shoreline-perpendicular preferential flow paths and wave-dominated delta deposits are more locally homogeneous, but scenarios for development of more pronounced shore-parallel heterogeneity patterns for wave-influenced deltas are discussed. The results highlight the need to consider the dual clinoform nature of wave-dominated delta deposition for facies prediction and subsurface interpretation.