The impact of polycyclic aromatic hydrocarbons (PAHs) on the marine food web is crucially understudied in the primary trophic system. We evaluated the seasonal dynamics of PAHs in microplankton in a polluted environment (Taiwan), northeastern South China Sea. Replicate size-fractionated microplankton (55–1000 μm) were freeze-dried, and PAHs were extracted with a 1:1 v/v ratio of acetone: n-hexane, then analyzed using GC–MS. Total PAHs ranged between 68 and 2548 ng/g dw in microplankton, greatest during spring (130–2548 ng/g), followed by autumn (135–772 ng/g) and summer (44–423 ng/g). Spatial distribution varied through seasons but was higher in the southern part (S6 > S4 > S5 > S2 > S3 > S1 > S7), dominated by higher-ring PAHs from mixed pyrogenic and petrogenic sources. PAHs are significantly correlated with environmental factors, especially in colder seasons and lower salinity areas. Suspended matter and plankton influenced PAH transport and partitioning seasonally. Plankton's PAHs seasonal changes and environmental influences are revealed in an anthropic environment.