Particulate algal toxins represent an emerging class of particle-associated pollutants that integrate in situ production, particle association, and trophic processing. However, their seasonal dynamics across planktonic food webs remain poorly understood in marginal seas. Using four seasonal surveys in the Yellow–Bohai Seas, we quantified diarrhetic shellfish poisoning (DSP) and paralytic shellfish poisoning (PSP) toxins in phytoplankton- and zooplankton-associated fractions. Phytoplankton-associated DSP (DSPp) was widespread (40–75% seasonally) with seasonal compositional variation, while PSP toxins (24–48%) shifted seasonally between N-sulfocarbamoyl gonyautoxins 1 and 2, and gonyautoxin-dominated profiles. Zooplankton-associated DSP (DSPz) was predominantly observed in summer with trophic transfer intensity peaking during this season. Two-stage generalized additive models revealed distinct controls on toxin occurrence versus intensity. Toxin detection was influenced by multiple factors, with temperature, salinity, nutrient concentrations, diatom biomass, and toxin-producing phytoplankton abundance each contributing over 20% at times, with nutrient levels and diatom biomass having a more pronounced effect on trends. DSPp concentrations were mainly driven by temperature, peaking at ~15 ℃, while DSPz concentrations were mainly governed by particulate DSP availability, with DSPp explaining ~27% of variability and triggering abrupt increases above ~700 pg L⁻¹. These results highlight the need for pollution-oriented monitoring frameworks that extend beyond toxic algal abundance to better assess ecological risks in coastal environments.