The mariculture industry has rapidly developed in recent decades owing to population growth and the increasing demand for seafood. Phytoplankton is an important indicator for assessing the carrying capacity of bivalve mariculture as well as a limiting factor for large-scale and high-density bivalve cultivation. Phytoplankton can be categorized by size into picophytoplankton (<2 μm), nanophytoplankton (2–20 μm), and microphytoplankton (20–200 μm). Considering that the retention rate of picophytoplankton by filter-feeding bivalves is very low, using the total amount of phytoplankton available for aquaculture capacity assessment would result in an overestimation. Therefore, understanding the particle size composition and spatiotemporal distribution characteristics of phytoplankton in the target sea area can improve the accuracy of assessing bivalve culture capacity and provide scientific guidance for marine bivalve aquaculture. Blue mussel Mytilus edulis and triploid oyster Crassostrea gigas are the most common bivalve species in Haizhou Bay, a typical bivalve mariculture area in China. This study aimed to understand the size-fractionated phytoplankton and its environmental influencing factors, including water temperature, salinity, dissolved oxygen, pH, total nitrogen, total phosphorus, phosphate, silicate, nitrate, nitrite, ammonia nitrogen, dissolved inorganic nitrogen, N/P, N/Si and Si/P, both in bivalve mariculture areas (Area 1 and 2) and non-mariculture areas (channel and reference areas). Phytoplankton biomass was investigated in March, July, September, October, and December 2023 by measuring Chl-a of size-fractionated phytoplankton. Two-way variance and redundancy analyses were used to analyze the effects of environmental factors on size-fractionated phytoplankton. (1) The annual variation range of total Chl-a concentration in the investigated area was 0.86–18.49 µg/L, and the seasonal difference was significant (P < 0.05). The annual ranges of pico Chl-a, nano Chl-a, and micro Chl-a concentrations were 0–0.90, 0.13–6.12, and 0.35–15.30 µg/L, respectively, with significant seasonal differences (P<0.01). However, no significant differences were observed in the concentrations of Chl-a in March (1.98±0.61 µg/L) and December (3.69±1.55 µg/L). In July and October, the average concentrations of Chl-a in Area 1 were (9.80±2.04) µg/L and (12.34±6.27) µg/L, respectively, which was much higher than those in other areas (P<0.05). This may be due to the higher nutrient concentration in the coastal waters. In September, the Chl-a concentration in Area 2 (1.47–1.94 µg/L) was significantly lower than in the non-bivalve mariculture areas (P<0.01). Simultaneously, the nitrate and nitrite concentrations in Area 2 were significantly higher than in the other areas. This period marked the rapid growth of bivalves and was presumed to be caused by bivalve feeding and excretion. (2) Phytoplankton communities exhibit notable spatiotemporal variation. In March, the phytoplankton communities of Area 1 and the channel area were dominated by microphytoplankton, whereas Area 2 and the reference area were dominated by nanophytoplankton. In July, nanophytoplankton dominated in Area 1 and the channel area, whereas microphytoplankton dominated in Area 2 and the reference area. In September, microphytoplankton dominated Area 1, Area 2, and channel area, whereas nanophytoplankton dominated the reference area. The proportion of picophytoplankton in the reference area was significantly higher than that in other areas (P<0.05). In October, the contribution rate of microphytoplankton increased gradually in all areas, and the value added in bivalve mariculture areas was significantly higher than that in the non-bivalve mariculture areas (P<0.05). In December, no significant difference was observed in the contribution rate of particle size in different areas, but the contribution rate of microphytoplankton continued to increase across different areas, with an average value of 89.01%. The contribution rate of picophytoplankton was mainly affected by seasonal factors (P<0.001), whereas the contribution rate of nanophytoplankton and microphytoplankton was significantly affected by seasonal and seasonal and regional interactions (P<0.05). (3) Seasonal and regional differences exist in the response of the particle size structure of phytoplankton to environmental factors in the survey areas. The redundancy analysis showed that the first two axes explained 79.31%, 86.94%, 88.35%, and 99.09% of the species variation in Area 1, Area 2, channel area, and reference area, respectively. Seasonal and regional differences influenced the response of the particle size structure of phytoplankton to environmental factors in the four areas. A significant negative correlation was observed between nanophytoplankton and N/Si in Area 1. In Area 2, picophytoplankton was significantly negatively correlated with total nitrogen, and nanophytoplankton was significantly positively correlated with N/P. In the channel area, the phytoplankton of three sizes were significantly negatively correlated with ammonia nitrogen. Microphytoplankton was positively correlated with DIN in the reference area (P<0.05). Consequently, nutrient salts mainly regulated the Chl-a concentration of phytoplankton in Area 1, whereas the effects of nutrient salts and cultured bivalve influenced the Chl-a concentration of phytoplankton in Area 2. For the entire survey area, seasonal changes in environmental conditions are the main cause of phytoplankton particle size structure variation. In addition, the presence of seasonal and regional interactions in nanophytoplankton and microphytoplankton suggests that bivalve farming may also affect the size-fractionated phytoplankton.