Incised-valley fills shallowly buried beneath the New Jersey middle–outer shelf reveal a retrogradational shift of four seismic facies, as observed in 1–4 kHz deep-towed chirp seismic data. These facies, the only preserved stratigraphic record of the latest Quaternary–Holocene drowning and infilling of fluvial drainage systems developed on this exposed shelf at or near the Last Glacial Maximum (LGM), are interpreted as (1) fluvial lag deposits, SF1; (2) estuarine mixed sand and muds, SF2; (3) estuary central bay muds, SF3; and (4) redistributed estuary-mouth sands, SF4. These fills are truncated by a transgressive ravinement, the T horizon, which is in turn overlain by Holocene marine sand deposits. The seismic facies are bounded by reflectors marking either source diastems or unconformities: (1) the Channels horizon is the lowstand fluvial incision surface, (2) B1 is a bay flooding surface, (3) B2 is an intra-estuarine depositional surface, (4) B3 is a tidal ravinement surface, and (5) the T horizon represents erosion at or near the shoreface during Holocene transgression. The Channels horizon is generally preserved only in valley axes. Elsewhere, this sequence boundary has been modified by surfaces B1 and/or B3. Dip-oriented changes in the thickness of SF3 and SF4 suggest either a stillstand in the passage of the shoreline, which allowed such spatial variations, or that local valley shape controlled hydrodynamic conditions for sediment transport and deposition. Narrower valleys may have promoted tidally dominated, fine-grained deposition within these drowning estuaries, while broader valleys attenuated tidal flow velocities and allowed the filling of the estuary to be dominated by wave and current energy, promoting more coarse-grained deposition. Our study demonstrates that wave- and tide-dominated estuarine facies can coexist within such fill strata.