Abstract: The modern subaqueous delta of the Huanghe (Yellow) River is an important area for oil and gas exploitation, submarine pipeline construction, offshore wind farming, and other infrastructure developments. The Huanhe River has undergone multiple shifts in its deltaic river course, resulting in significant variations in sediment supply, ocean dynamics, and human activities in different river mouth areas. Based on the data from subbottom profiler and multibeam echo-sounder in 2022 and 2023, we investigated the spatial distribution of shallow-strata disturbances in the delta and its subordinate areas (the Diaokou-Shenxiangou river mouth, the modern river mouth, and the Qingshuigou river mouth). Differences in disturbances among the three areas were examined. The main controlling factors of the disturbances were revealed by combining data on sediment supply and ocean dynamics in different river mouth areas. Results show that (1) the shallow-strata structure of the delta exhibits significant spatial variability. The number of disturbed strata in the delta decreased with increasing water depth. The disturbances in various river mouth areas differed from each other significantly. The Diaokou-Shenxiangou river mouth is characterized by numerous disturbances in shallow burial depth. The Qingshuigou river mouth is characterized by disturbances in clustered distribution, shallow burial, and large development scale. The modern river mouth are characterized by deep burial and less disturbance. (2) The shallow-strata structure of different areas of the delta was significantly influenced by factors such as sediment input and ocean dynamics, exhibiting distinct spatial differences. The field of high bottom-shear stress of waves is highly consistent with the distribution of high-density stratigraphic disturbance, indicating that wave-induced bottom shear stress was the main dynamic factor affecting the differences in stratigraphic structure in the three subordinate estuarine areas at different water depths.