For decades, in response to industrialization and urbanization, environmental qualities of estuarine and coastal areas of the west coast of Korea have been deteriorating. Long-term changes in concentrations of persistent toxic substances (PTSs) in sediments, including PAHs, styrene oligomers, nonylphenols, and metals and their potential toxicities via AhR- and ER-mediated potencies, and bioluminescent bacterial inhibition, were investigated. Long-term monitoring in five estuarine and coastal areas (2010-2018; 10 sites) showed that concentrations of PAHs and nonylphenols in sediments have declined while concentrations of some metals, Cd, Cr, and Hg have increased. Similarly, AhR-mediated potencies in sediments have declined, but inhibitions of bioluminescent bacteria have increased. Concentrations of sedimentary PAHs and AhR-mediated potencies were significantly (p < 0.01) and positively correlated. Sources of PAHs from combustion have been gradually declining while inputs from vehicle exhaust by-products have been increasing. Overall, this study brought our attention a balanced regulation in chemical-specific manner.