Since 6 kyr BP, the subaerial deltas of the Yellow, the Yanshan and the Taihang river systems evolved along the Bohai Bay coast, forming several lobate progradational systems associated with frequent avulsions of these river systems. Their subaqueous parts consist of a multi-sourced subaqueous deltaic complex in Bohai Bay, but little is known about the complex's subsurface structure, morphology and evolutionary history. Here we investigate these characteristics using a dense, high-resolution seismic survey. Using stratigraphic superposition, seismic geometry, and the results of previous studies, we identified nine seismic units (SUs) in the post-Last Glacial Maximum stratigraphy, which are interpreted, from bottom to top, as: (1) fluvial/lacustrine sediments (SU0); (2) marine sands combined with estuarine/coastal deposits (SU1); and (3) a subaqueous fluviodeltaic complex (SUs2–8); these units correspond to the lowstand system tract, the transgressive and/or highstand system tracts, and the normal regressive system tract, respectively, and evolved as a function of eustatic fluctuations. The subaqueous fluviodeltaic complex is characterized by a discrete and spatially-confined lobate architecture, which is indicative of step-wise switching of subaqueous lobes. Two sets of progradational systems (PS), a northern one (SUs2–3) and a southern one (SUs4–8), were observed within the complex, tapering in opposite directions and bounded by an erosional unconformity (R3). These characteristics indicate that the two PS were sourced from different river systems and prograded at different times. R3 forms the base of the southern PS but cross cuts the northern PS, indicating that it is a diachronous surface marks the preexisting seafloor, which was further reworked/eroded by the progradation of the southern PS. In each PS, the internal subaqueous lobes correlated well with the onshore lobes/superlobes of the subaerial deltas, suggesting the lobate evolution of the complex is driven predominantly by alternating erosion and deposition caused by the variation in fluvial supply, which appears to be linked to the frequent avulsions of the major river systems, in addition to the multi-sourced supply. Based on the dipping geometries and the locations of the depocenters, we hypothesize that (1) the northern PS is the seaward extension of the ancient Haihe River's northern branch; (2) the bulk of southern PS in the middle and southern Bohai Bay is correlated with the principal body of the Yellow River subaqueous delta; (3) the majority of the volume of the northern PS in northern Bohai Bay consists of the modern Haihe River subaqueous delta.