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<p>The global ocean's coastal areas are rapidly experiencing the effects of climate change. These regions are highly dynamic, with relatively small-scale circulation features like shelf break currents playing an important role. Projections can produce widely diverging estimates of future regional circulation structures. Here, we use the northwestern North Atlantic, a hotspot of ocean warming, as a case study to illustrate how the uncertainty in future estimates of regional circulation manifests itself and affects projections of shelf-wide biogeochemistry. Two diverging climate model projections are considered and downscaled using a high-resolution regional model with intermediate biogeochemical complexity. The two resulting future scenarios exhibit qualitatively different circulation structures by 2075 where along-shelf volume transport is reduced by 70 % in one of them and while remaining largely unchanged in the other. The reduction in along-shelf transport creates localized areas with either amplified warming (<span class="inline-formula">+3</span> <span class="inline-formula">^∘</span>C) and salinification (<span class="inline-formula">+0.25</span> units) or increased acidification (<span class="inline-formula">−0.25</span> units) in shelf bottom waters. Our results suggest that a wide range of outcomes is possible for continental margins and suggest a need for accurate projections of small-scale circulation features like shelf break currents in order to improve the reliability of biogeochemical projections.</p>