<p>Assessing food web dynamics is crucial for understanding the impact of climate change on Antarctic coastal ecosystems. We assessed the spatial heterogeneity of biodiversity and food web structures in Marian Cove, Antarctica, an area that is experiencing rapid ecological change, by analyzing multiple genetic loci from environmental DNA. Biodiversity in Marian Cove varied distinctly between the inner and outer coves, which correlated with the physicochemical properties of seawater influenced by glacial retreat. The size composition of primary producers, represented by diatoms in the outer cove and nano- or pico-phytoplankton in the inner cove, was identified as the core taxa in each food web. The food web in the inner cove was primarily driven by bottom-up regulation, with smaller phytoplankton size classes responding to environmental fluctuations, in contrast to the outer cove, which was primarily influenced by oceanic water with large diatoms that enhanced the food web structure stability. Our study enhances the understanding of food web dynamics in Antarctic coastal ecosystems in response to glacial retreat driven by climate change.</p>