Abstract: The rapid development of the marine economy has been accompanied by increasing deterioration of coastal water quality. Lianyungang, an important seaport city in Jiangsu Province, has experienced rapid growth in recent years in sectors such as ports and shipping, coastal industries, and marine aquaculture. However, human activities have resulted in increasing levels of nitrogen (N) and phosphorus (P) pollution in its nearshore waters. This study used water-quality monitoring data collected from nearshore waters and major river estuaries in Lianyungang in 2020 to investigate the spatial distribution, source contributions and marine input fluxes of total nitrogen (TN) and total phosphorus (TP). Multivariate statistical analysis and the absolute principal component score–multiple linear regression (APCS-MLR) model was used to apportion sources, while the export coefficient method and a retention coefficient model were used to estimate the emissions of TN and TP into the sea and their fluxes into the sea. The results showed that the concentrations of TN and TP in the Coastal Waters of Lianyungang City generally decreased from the nearshore to the offshore areas. High TN concentrations were mainly found in the estuaries of the Chezhou River, Xinyi River and Guan River, and in Haizhou Bay, whereas high TP concentrations were primarily found in the estuaries of the Xinyi River and Guan River, Lianyungang Port, and the southern part of Haizhou Bay. The source apportionment results identified agricultural activities as the dominant source of both TN and TP, with chemical industries and land-port transportation activities identified as secondary contributors. In 2020, the estimated emissions of TN and TP in Lianyungang City were 23 890.36 t and 1 868.41 t, respectively. The highest TN emissions were observed in Guannan County, while the highest TP emissions were found in Donghai County. The measured TN and TP fluxes into the sea from Lianyungang City was 53 662.53 t and 3 884.40 t, respectively. By comparison, the estimated fluxes based on model were 60 149.27 t for TN and 3 269.65 t for TP, corresponding to relative errors of 10.78% and 18.80%, respectively. According to the model estimates, the estimated upstream inflow of TN and TP fluxes into the sea was 43 811.73 t and 2 221.15 t, respectively, while the estimated locally generated fluxes of TN and TP from Lianyungang City was 16 337.54 t and 1 048.50 t, respectively. Among the estimated locally generated fluxes of TN and TP, livestock and poultry farming, as well as agricultural fertilizers, were identified as the major contributors. The relatively high estimated TN and TP fluxes into the sea were mainly concentrated in the Xinmu River and Tongyu River basins, the Xinyi River and Guan River basins, as well as in Lianyun District, Guannan County, and Donghai County. This study provides a scientific basis and decision support for pollution control at the source and integrated management of nearshore ecological and environmental protection in Lianyungang City within the framework of coordinated land and sea management.