Estuaries, vital coastal ecosystems, face growing threats from industrialization. To understand the pace of sedimentary changes and heavy metal pollution at the anthropogenically altered and industrialized Nakdong River Estuary in South Korea, we used sediment coring to reconstruct environmental change. Estuarine dam construction in 1934 shifted the sedimentary system from sand to mud, coinciding with a post-1930s mercury increase due to coal burning. Mercury concentrations in other South Korean regions surged in the 1970s, indicating proximity to emission sources matters. However, most heavy metal levels (Cu, Cd, Zn, Ag) sharply rose in the 1960s and 1970s with regional industrialization. Modern heavy metal concentrations doubled pre-industrial levels, underscoring human activities as the primary driver of Nakdong Estuary environmental changes. This emphasizes the need for a balanced approach to development and environmental preservation.