Allochthonous nutrient subsidies play an important role in shaping biotic communities, particularly in naturally oligotrophic ecosystems such as those commonly found in the Canadian High Arctic. Seabirds have been identified as an important vector capable of transporting significant quantities of nutrients from marine to terrestrial environments. However, the influence of seabird-derived nutrients on water quality and ecosystem functioning of Arctic freshwater systems has been largely unexplored. Here, we sampled 24 ponds on Cape Vera, Devon Island (Nunavut, Arctic Canada), an area that is home to over 10,000 nesting pairs of northern fulmars (Fulmarus glacialis), in order to explore the influence of seabirds on water quality and diatom ecology. Our data reveal distinctive water chemistry changes (e.g., high pH, nutrients) and diatom assemblages (e.g., very low diversity) related to varying degrees of bird influence. Using δ¹⁵N as a proxy of trophic level, we show that a small but significant portion of the variance in the diatom species data can be explained by seabird-derived nutrients. Although the generation of robust quantitative models predicting δ¹⁵N from fossil diatom data was limited by the overwhelming dominance of a few taxa, this study provides evidence that seabird-derived nutrients play a critical role in influencing the water quality of Arctic ponds. Interestingly, diatom assemblage composition does not respond in a simple fashion to seabird-derived nutrients, in contrast to diatom–nutrient relationships recorded in many temperate regions.