Estuaries are susceptible to both anthropogenic disturbances and global climate changes. Impacts may be discriminated by pollution patterns of widely quantified persistent organic pollutants (POPs), though data are scarce for extreme climate events. This study quantified four groups of POPs, i.e., polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), dichlorodiphenyltrichloroethanes (DDTs), and hexachlorocyclohexanes (HCHs), in sediments from seven Chinese coastal estuaries across a gradient of socioeconomic development in their watersheds with comparisons among the pre-typhoon, typhoon, and post-typhoon periods during 2016–2019. The maximal average concentrations, up to 1561 μg PAHs kg−1, 235 μg DDTs kg−1, and 38.9 μg HCHs kg−1, were quantified in the Jiulong River estuary and 7.61 μg PCBs kg−1 in the Jiao River estuary. Anthropogenic activities contributed to the distinctive spatial distributions of four groups of POPs in estuaries with non-agricultural gross domestic product (NAGDP) per capita significantly relating to sedimentary concentrations of PAHs and PCBs and agricultural gross domestic product (AGDP) per capita relating to DDTs and HCHs. Seasonality and typhoons led to less temporal variations in sedimentary POPs concentrations, whose spatial heterogeneity was remarkably reduced in the post-typhoon period rather than in the pre-typhoon and typhoon periods. The results of this study suggested that fingerprinting legacy POPs in spatial and temporal distributions contributed to identifying the effects of anthropogenic disturbances and climate changes on estuarine sediment quality.