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Efforts to reduce land‐based non‐point source (NPS) pollutions from watersheds to coastal waters are ongoing all around the world. In this study, annual yield of NPS nitrogen (NPS‐N) pollution in Jiaodong Peninsula, China from 1979 to 2008 was estimated. The results showed that: from 1979 to 2008, NPS‐N yields exhibited significant inter‐annual variations and an increasing trend on decadal scale. High NPS‐N yield was mainly found in east and south parts, as well as the urbanized coastal regions in Jiaodong Peninsula. Among the 32 river basins, the three largest basins yielded more than 41.16% of the NPS‐N. However, some small coastal watersheds along the South Yellow Sea and Jiaozhou Bay had higher per unit area yield. Most of the small watersheds characterized by seasonal runoff had coastal waters pertain to mild and moderate pollution levels. The ratio of watershed area to shoreline length and the up‐stream land use had significant impacts on NPS‐N flux through the shoreline. Among the four adjacent coastal areas of Jiaodong Peninsula, Jiaozhou Bay was the most noteworthy one not only because of high levels of land‐based NPS‐N pollution but also because of its nearly enclosed structure. The combination between integrated coastal zone management and integrated river basin management, land use planning and landscape designing in Jiaodong Peninsula is recommended. Copyright © 2013 John Wiley & Sons, Ltd.