The coastal waters around the northern part of Zhejiang Province are confronted by serious environmental threats caused by the rapid development of the economy and highly efficient use of marine resources. In order to reduce and mitigate the possible negative effects of larger sea-related projects on the marine ecological environment, we built an evaluation index system to assess the offshore ecological environmental quality by analyzing the complexity and high turbidity of the water around the northern part of Zhejiang Province, as well as implementing an AHP (Analytic Hierarchy Process)-method based on three aspects: water environment, depositional environment, and marine biodiversity. We used the entropy weight method to determine the weight of the relevant factors, and used the comprehensive index weighting method to calculate the marine ecological environment comprehensive index (S). When S ≥ 75, it implies that marine ecosystem is healthy; when 60 ≤ S < 75, it suggests that marine ecosystem is sub-healthy; And when S < 60, it indicates that the marine ecosystem is unhealthy. On the basis of this, we integrated GIS spatial analysis methods with a mathematical model to practically study, on a macro scale, the coastal water around the northern shores of Zhejiang Province from 2009 to 2012. The results were as follows: (1) the ecological environmental quality of the coastal water around the northern shores of Zhejiang Province are in an unhealthy state, especially in Hangzhou Bay, Xiangshan Harbor, Sanmen Bay, and Ningbo-Zhou Shan sea area. The high inorganic nitrogen and phosphate contents and weak ocean primary productivity are the main factors affecting the quality of this environment. These factors cause high organic pollutant index values, high levels of eutrophication, and serious marine pollution in this area. (2) The hotspot analysis results showed that the pollutants are mainly concentrated in the Ningbo-Zhou Shan coastal waters, Hangzhou Bay, Sanmen Bay, and some other river estuaries. These regions have poor biological survival and low biodiversity due to economic development, construction of large sea-related projects, overfishing, and serious water pollution. In addition, the complexity and high turbidity of the water around the northern shores of Zhejiang Province cause weak ocean primary productivity, which affects the health of the entire ecosystem. (3) The analysis indicated that the unhealthy areas are mainly distributed in the vicinities of the coast, estuaries, and harbors, and the distribution of these areas with low ecological environment quality is similar to the human activities pattern, which suggests that human activities are the main factors affecting the health status of this marine ecosystem. In general, ecological environment quality in the coastal waters around northern Zhejiang Province progressively worsened between 2009 and 2012. This empirical study shows that the index system constructed for eco-environmental quality assessment and the method adopted reflects the actual state of a particular ecosystem and the internal relationships of the ecological system. Furthermore, our study results can provide a scientific basis for improving ecological environmental quality in the northern coastal waters of Zhejiang Province.