Three sedimentary systems tracts (LST, TST, and HST) have been identified in Nha Phu Bay and the adjacent shelf, Khanh Hoa Province, Vietnam. These have been deposited since the Last Glacial Maximum (LGM) and interpreted in this study via the analysis of high-resolution acoustic data and sediment cores. The lowstand systems tract (LST) comprises sandy sediments exposed at seabed on the outer shelf as sand ridges, and underlying the transgressive systems tract (TST) on the middle shelf. The LST developed under shallow-marine settings during the sea-level lowstand and early sea-level rise before 14.6 cal kyr BP. The TST comprises primarily fine-grained sediments deposited during the transgression between 14.6 and 8.0 cal kyr BP in an incised trough of the outer shelf, on the middle shelf, and in Nha Phu Bay. Erosion of the seaward portion of the TST on the middle shelf might occur during the late transgression (9.0–8.0 kyr BP). The highstand systems tract (HST) comprises sediments deposited during the sea-level highstand between 8.0 and 0.0 cal kyr BP and is distributed widely in the bay, on the inner-middle shelf, and partially on the outer shelf. A paleo-coast zone, located in 100–120 m present-day water depth, is recognized through the appearance of sand ridges and sandy sediments. The seafloor sediment distribution is mapped via four major acoustic echo types, combined with seabed sediment samples. The coarse-grained sediment distribution, subaqueous outcrops, and thin deglacial sediment thickness on the inner shelf indicate erosion-dominated processes under vigorous hydrodynamic conditions. Nha Phu Bay and the middle shelf are interpreted as the depocentres. The estimated sediment load deposited in Nha Phu Bay is 0.18 Mt./yr, accounting for 15–35% of the annual sediment discharge from the Dinh River. The seabed morphology, muddy sediment distribution, and deglacial sediment thickness reveal a dominant sediment-transport pathway, across the inner shelf to the middle shelf, near the northern shoreline of Nha Phu Bay under the influence of the southwest monsoon.