Water quality of rivers and coastal water bodies is very important to the development of Shandong peninsula blue economic zone. At present, water pollution degree has been decreased through strict management and many environment steps adaptation by local government. However, there are still some problem need to be solved, such as the management of downstream to estuary, division of riverine and marine region and different Standards for water/sediment quality and analysis. A comprehensive management model of “river-estuary-coastal zone” should be selected to protect coastal water quality. Making corresponding analysis methods and principles are of great significance to protect water quality, contributing to the blue economic zone of Shandong Peninsula. Furthermore, study of coastal theories and techniques should be strengthened to realize coordinate development of economic and environmental protection.