In recent decades, environmental degradation and unbalance of the embayment ecosystems caused by intense anthropogenic activities have threatened sustainable management of social and economic development in coastal areas. Nutrient input caused by human activities is a key factor affecting the ecological environment of the embayments. Therefore, transportation and transformation of nutrients and how these processes impacting on eco-environment being and in the involved mechanisms of embayments have been attracting the most of international attention in marine eco-environmental research. Nowadays, the main development trends in the embayments’ eco-environment research areas are: ①from phenomenon investigations of environmental quality and also biological community structure to environmental change mechanism and response mechanism of ecosystem structure and function; ②from fragment study of the eco-environment in the embayments to the ecosystem process and integrated system research; ③from the simple study of water to land-ocean interaction, and proposing the management requirements of integration of sea and watershed; and ④from short-term research of ecological environment to a long-term continuous variation study. Thus, the focus of the present study is mainly on: ①revealing the patterns of transportation and transformation of various nutrients in semi-closed bays under long-staying and long retention conditions; ②understanding the affecting processes and underlying mechanisms of nutrient variations on the community structure and function in the embayments; and ③establishing an integrated ecosystem-based management theory system.