The goal of this study was to experimentally assess the coupling between primary producer biomass dynamics and the distribution and fate of persistent organic pollutants (POPs) in a lake pelagic ecosystem. This was done by following the short-term evolution of polychlorinated biphenyl (PCB) concentrations in water and biota (phytoplankton and zooplankton) and the variability of bioconcentration (BCF), biomagnification (BMF), and bioaccumulation (BAF) factors during the development of a typical spring ecological progression in which the phytoplankton bloom is followed by a peak in the zooplankton abundance. The bulk of compounds with log KOW > 6.5 in the lake epilimnion was mainly associated with primary producer biomass. The phytoplankton biological pump was a major driver of POP export from the epilimnion, causing the decline of dissolved-phase concentrations. The BCF of phytoplankton for the more hydrophobic PCBs showed minima during the period of biomass climax. The concentration in the zooplankton of all selected PCBs sharply declined from March to May, with BAFs having minima in the post algal bloom phase. Biomagnification occurred during the pre algal bloom and algal bloom phases but appeared to be absent during the post algal bloom. This study highlights the occurrence of a prompt and complex response in the fate and distribution of POPs to dynamic biogeochemical control. Within the frame of the ecological succession, phytoplankton and zooplankton biomass dynamics produced bioaccumulation metrics varying over 1–2 orders of magnitude in the time frame of a few weeks and resulted in reduced trophic web exposure.