Sishili Bay is located in the northern Yellow Sea, China, and has importance for Yantai City as an aquaculture and tourism area. However, the rapid progress of the coastal economy has led to significantly deleterious effects on the inshore environment. The nutrient load and chemical oxygen demand has clearly increased within the bay, resulting in eutrophication and ecological imbalance. Harmful algal blooms have occurred frequently in recent years, resulting in heavy economic losses. Nutrient structure and trophic level may play an important role in phytoplankton ecology. To understand the effect of trophic state on phytoplankton diversity within the bay, a survey was carried out from 2006-2010. Six sampling sites were chosen, and nutrient composition, trophic state, organic pollution and phytoplankton quantity and diversity were studied in the months of May, August and October over the study period. Sampling and testing methods followed that of the Specifications for Oceanographic Surveys and Specifications for Marine Monitoring. Significance testing and the correlativity between the investigated parameters were analyzed using SPSS 17.0. The results showed that nitrogen/phosphorus (N/P) ratios increased during the initial part of the study period, and then decreased in recent years. Between 2008 and 2009, N/P ratios wee generally higher than during the other periods, with the maximum ratio value of 162.05 occurring in May, 2009. Oligotrophic-medium trophic levels with an inorganic phosphorus (IP) limit usually occurred during May and August, while conditions of potential eutrophication with an IP limit usually occurred in October. With the exception of slight organic pollution (level three, 2<A≤3) and a moderate pollution (level four, 3<A≤4) determined in October 2006 and 2007 respectively, organic pollution was seldom detected during the other survey periods. Consequently, it was suggested that organic pollution within Sishili Bay may be gradually ameliorated. Phytoplankton quantity and harmful algal bloom occurrence were higher in 2008-2009. The diversity index (Shannon-Wiener index H') of phytoplankton fell during the study period up to 2009, but subsequently got higher. However, the change in phytoplankton quantity showed an inverse relationship to diversity. Correlation analysis revealed a positive and significant correlativity between the organic pollution index (A) and the IP concentration in seawater (P < 0.01) (the regression equation was: A=0.1105 IP-0.3365, R=0.753, n=90). A positive correlation coefficient was determined between the organic pollution index (A) and the dissolved inorganic nitrogen (DIN) concentration (P > 0.05). This indicated that IP was a major influencing factor of organic pollution within Sishili Bay. Phytoplankton diversity had a negative correlativity with phytoplankton quantity, but a positive correlation coefficient with the Si/P ratio (Pearson correlation coefficient of 0.446) and IP concentration (Pearson correlation coefficient of 0.413) (P > 0.05). IP may be the primary impact factor determining the trophic state, organic pollution status and phytoplankton diversity within Sishili Bay. Eutrophication and the unbalanced nutrient composition within Sishili Bay may have a negative impact on primary production and ecosystem health within Sishili Bay. The effect of anthropic activity on the bio-diversity and ecological health of the bay should be better understood, so as to achieve sustainable development of marine resources.