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Algal bioindicators, such as diatoms, often show subdued responses to eutrophication in Arctic lakes because climate‐related changes (e.g., ice cover) tend to be the overriding factors influencing assemblage composition. Here, we examined how sub‐Arctic ponds historically receiving high nutrient inputs from nesting seabirds have responded to recent climate change. We present diatom data obtained from 12 sediment cores in seaduck‐affected ponds located on islands through Hudson Strait, Canada. All study cores show consistently elevated values of sedimentary ẟ¹⁵N, an established proxy for tracking marine‐derived nutrients, indicating seabirds have been present on these islands for at least the duration of the sediment records (~100 to 400 years). We document diverse epiphytic diatom assemblages to the base of all sediment cores, which is in marked contrast to seabird‐free Arctic ponds—these …