Phytoplankton, which serve as primary producers within marine ecosystems, exhibit rapid responsiveness to ecological shifts in aquatic environments. Thus, they play a pivotal role in maintaining the health and stability of these systems. China is a leading aquaculture nation boasting approximately 70% of global aquaculture output, with shellfish accounting for 72% of total production. Phytoplankton serve as the primary food source for shellfish, which regulate their biomass through filter feeding mechanisms. Furthermore, the excretions from shellfish modify nutrient concentrations in the water, indirectly influencing the composition of phytoplankton communities and consequently impacting water quality and overall ecosystem health. By examining the intricate relationship between shellfish and phytoplankton and exploring the ramifications of shellfish farming activities on phytoplankton populations, we can anticipate and address the potential effects of marine environmental changes on aquaculture. This endeavor is crucial for assessing ecological carrying capacity and planning shellfish farming activities, thereby ensuring a harmonious balance between marine economic development and ecological preservation. Haizhou Bay, located between the southern part of the Shandong Peninsula and the northern part of Jiangsu Province, has shellfish and Porphyra as its main farming species, with shellfish being the predominant species. However, few studies focused on the relationship between shellfish culture and phytoplankton Thus, this study aimed to explore the effects of a mixed cultivation of oyster and mussel, and marine environmental factors on phytoplankton community structure. Surveys of phytoplankton and environmental factors in Haizhou Bay were investigated in March, July, September, October, and December 2023. The survey was divided into four areas: Area 1, Area 2, waterway, and offshore. Areas 1 and 2 served as aquaculture areas, whereas the waterway and offshore areas served as non-aquaculture areas. The shallow-water type Ⅲ plankton network was used to vertically dragged from the seabed to the sea surface to collect phytoplankton biological samples. Environmental factors of sea surface and bottom were investigated, and the average value was calculated for data analysis. Two-way analysis of variance was performed on environmental factors and phytoplankton communities for seasonal and regional changes. Canonical discriminant analysis (CDA) was used to analyze the similarity of phytoplankton community structure in different areas, and redundancy analysis (RDA) was conducted to study the relationship between predominant phytoplankton species and environmental factors. Significant seasonal differences in temperature, salinity, pH, dissolved oxygen, chemical oxygen demand, and nutrient concentration were observed in the survey area (P＜0.001). Water temperature and salinity were affected by terrestrial inputs. In July, September, and December, the nutrient salt concentrations in Areas 1 and 2 were higher than those in the other regions. A total of 69 species of phytoplankton in 33 genera and 3 phyla were identified in the survey area, with Bacillariophyta being the predominant group, accounting for 87% of the species. Fourteen dominant species appeared in the survey, including Chaetoceros lorenzianus, Chartoceros sp., Coscinodiscus grannii, and Skeletonema costatum, most of which belonged to Bacillariophyta, with significant seasonal and regional variations. Significant differences in phytoplankton abundance (1.40×10⁴ –739.11×10⁴ cell/m³ ) were found between seasons and regions (P＜0.05). After the red tide in September, the abundance of phytoplankton decreased compared with that in July and reached the highest value in October. Affected significantly by terrestrial inputs, the abundance in Area 1 was higher than that in the other areas in all seasons, and the surveyed area generally had higher abundance of nearshore phytoplankton than the offshore area. Significant regional and seasonal differences in species diversity index were found (P＜0.05). The survey conducted in September, following the occurrence of a red tide, showed that the phytoplankton diversity index was higher in the aquaculture areas than in the non-aquaculture areas. Although some oysters died, the proportion of remaining shellfish in farming was still significant, and shellfish activities possibly increased the stability of the phytoplankton community to a certain extent. CDA results showed that the similarity of phytoplankton community structure between the aquaculture and offshore areas was low, and shellfish activities can influence the composition of the phytoplankton community structure. The waterway area, due to its proximity to the bay and slower water exchange, had a high similarity in phytoplankton community structure to Area 2. RDA results showed that the abundance of dominant species of phytoplankton were affected by environmental factors such as temperature, pH, NO3-N concentration, and NO2-N concentration, and the abundance of dominant species positively correlated with nutrient concentration in July, September, and October. In Area 1, environmental factors such as water temperature and salinity and nutrient concentration were greatly affected by terrestrial inputs, and the changes in phytoplankton community in this area may be affected by geographical location and shellfish farming activities. This study preliminarily explored the relationship between phytoplankton and environmental factors in shellfish culture area, and its results may serve as a basis for shellfish culture planning and aquaculture capacity assessment in Haizhou Bay.