Seabirds are biovectors that transport large concentrations of nutrients from their marine feeding areas to terrestrial breeding grounds. Here, we used subfossil cladoceran assemblages to assess if, and how, changes in the world’s largest colony of Leach’s Storm Petrels affected the structure of Cladocera assemblages over the past ~1700 years. Using sediment cores from four ponds impacted by Leach’s Storm-Petrel colonies on Baccalieu Island (NL, Canada), we observed a consistent transition in cladoceran assemblages from benthic/littoral to pelagic taxa in association with high seabird presence. This shift aligns with previously published limnological changes that tracked the growth of the colony. Compared to trends in sedimentary chlorophyll-a, pelagic cladoceran taxa lagged behind algal shifts driven by seabird activity. The main drivers of cladoceran assemblage shifts were likely alterations to the physical habitat structure and food availability driven by seabird inputs. Furthermore, deposition of calcium from seabirds may have also contributed to changing the composition of cladoceran communities. Our study provides information on food web shifts associated with seabird-driven eutrophication, which can be compared to future paleoecological studies.