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Nitrogen loading has been linked to eutrophication and seagrass bed declines worldwide, yet early warning signs and potential mitigating factors are often less clear. Our objective was to use published nitrogen loading model results together with eelgrass habitat surveys from 7 bays in Atlantic Canada to assess linkages between nitrogen loading, tidal flushing and bivalve aquaculture on observed eutrophication indicators in eelgrass habitats. Field surveys revealed significant differences in primary indicators (annual algae, tissue nitrogen) and secondary changes in eelgrass bed structure, yet no large loss of eelgrass cover or biomass. Multivariate analyses found positive correlations between nitrogen loading and eutrophication indicators, with distinct clusters of high- and low-impact sites, and the mitigating effects of flushing time and aquaculture. Our results highlight that combining measures of nitrogen loading, eutrophication indicators and mitigating factors can help detect early warning signs and assess eutrophication risk to inform management and conservation of coastal ecosystems before significant losses of seagrass occurs., (Copyright © 2018 Elsevier Ltd. All rights reserved.)