Abstract: Intensifying human activities within large river basins have significantly altered the transport processes of riverine heavy metals to the sea, necessitating systematic investigations into their sedimentary effects in estuarine and adjacent coastal areas. The implementation of the Water-Sediment Regulation Scheme (WSRS) in the Yellow River provides an ideal case study for this purpose. Based on a comparative analysis of sediment composition and heavy metal concentrations in the Yellow River estuary and its adjacent sea areas during a WSRS period (July 2023) and under natural conditions (May 2021), this study identified significant changes in heavy metal concentrations and distribution patterns in surface sediments during the WSRS compared to the natural conditions. The dominant controlling factors and underlying mechanisms were explored, revealing the profound impact of this major human activity on the sedimentary processes of metals entering the sea from the Yellow River. The results indicate that, relative to natural conditions, heavy metal concentrations in surface sediments of the study area were markedly higher during the WSRS, with more pronounced spatial heterogeneity and a substantial expansion of areas with elevated concentrations. This significantly altered the distribution pattern of heavy metals. Although pollution assessment indices remained at relatively low levels, they showed a clear increasing trend. Changes in sediment source, grain size, and major components were the primary factors controlling heavy metal content and distribution. This study reveals that the Water-Sediment Regulation Scheme (WSRS) alters the heavy metal deposition patterns primarily through three mechanisms: shifting sediment provenance from coarse-grained material from the lower river channel to fine-grained, heavy-metal-enriched sediments from the middle-reservoir impoundments; inducing intense hydrodynamic disturbances and rapid sedimentation, which weaken the grain-size control; and activating the geochemical processes of reactive carriers such as iron oxides and calcite. Collectively, these processes lead to increased heavy metal concentrations and a pronounced reorganization of their spatial distribution patterns. This research holds significant scientific value for deepening the understanding of sedimentary processes and environmental effects of heavy metals and other pollutants in large river estuaries and deltaic regions under the influence of intense human activities. It also provides theoretical support for the sustainable management of estuarine environments.