Abstract: Fronts in the Changjiang River Estuary-coastal continuum play a critical role in regulating hydro-chemical-biological processes; however, a systematic understanding of their spatiotemporal variability and ecological consequences remains limited. Based on in situ investigations and remote sensing data collected in April and August 2021, this study characterizes the spatial distribution and seasonal evolution of frontal systems within the Changjiang River Estuary–coastal continuum and elucidates their regulatory mechanisms on material transport, Chlorophyll a (Chl-a) distribution, and hypoxia. The results reveal a nested frontal structure where thermal fronts, which are driven by the southward intrusion of the western Yellow Sea Coastal Current in spring and coastal upwelling in summer, are interposed between the spatially segregated turbidity and plume fronts. The decoupled transport of suspended particulate matter and nutrients induced by the turbidity and plume fronts favors the formation of a high Chl-a zone between these two fronts. The nested cold water intrusion (spring) and upwelling (summer) supply additional nutrients and reshape the spatial pattern of high Chl-a. Meanwhile, net desorption of phosphate from suspended particles within the turbidity maximum zone on the inshore side of the turbidity front leads to elevated phosphate concentrations. In summer, the spatial extent of low-dissolved-oxygen bottom water is strongly modulated by the turbidity and plume fronts, whereas the nested upwelling regulates the vertical distribution and evolution of hypoxic water. This study provides a scientific basis for understanding the regulatory effects of frontal systems on material transport and their eco-environmental impacts in the Changjiang River Estuary–coastal continuum.