Abstract: Under global climate change and intensifying human activities, estuarine and coastal ecosystems are facing multiple environmental challenges, including eutrophication, hypoxia, and acidification, making them a frontier focus in current marine environmental research. This paper systematically reviews the driving mechanisms behind low oxygen and acidification, focusing on key processes such as nutrient enrichment, water column stratification, organic matter sedimentation, and microbial remineralization. It further summarizes the response characteristics of coastal community structures under coupled hypoxia-acidification conditions and their impacts on biogeochemical cycles. By examining case studies from typical regions—including the Yangtze River Estuary, Pearl River Estuary, Chesapeake Bay, and the Baltic Sea—the paper identifies regional differences and evolutionary trends in nutrient sources, hydrodynamic conditions, and ecological responses across different coastal zones. Addressing major challenges in current coastal ecosystem management—such as insufficient cross-regional coordination, mismatched governance scales, and delayed ecological restoration—the paper proposes an integrated "watershed–estuary–coastal" management framework. This approach emphasizes enhanced land-sea integration and regional collaboration, improves regulation of ecological processes, and strengthens long-term monitoring systems to enhance the resilience and safety of coastal ecosystems, thereby providing scientific support for sustainable coastal environmental management.