Parasites of phytoplankton influence phytoplankton bloom dynamics and may severely affect the type of food available for higher trophic levels. The incidence of parasitic infections generally is expected to increase across ecosystems worldwide under the scenario of global change. Herein we report on a massive parasite infection on two dominant diatoms of the austral winter bloom, namely Thalassiosira pacifica and Chaetoceros diadema, recorded during an extreme precipitation period in the Bahía Blanca Estuary, Argentina. The parasite infection was concomitant with a marked drop in water salinity and affected more than 40% of host cells. Although the parasite on C. diadema was not identified, the parasite on T. pacifica was most likely Pirsonia sp., a nanoflagellate with high host specificity. After the intense rainy period and the parasitic infection, the phytoplankton biomass dropped (by more than 80%) and the community structure shifted to one with smaller species (i.e. Thalassiosira curviseriata, T. hibernalis and T. minima). We discuss the implications that these modifications may have on the food web dynamics and the potential relationship between precipitation-driven modifications in water properties and the emergence of parasitism in coastal eutrophic environments.