ABSTRACT: In this paper, we explicitly link changes in community structure of estuarine primary producers to measured nitrogen loading rates from watersheds to estuaries, and quantify the relationship between nitrogen load, annual dynamics of algal growthand Zostera marina L. productivity, and overall eelgrass decline at the watershed-estuarine scale in estuaries of Waquoit Bay, Massachusetts, USA. Substantial eelgrass loss (80 to 96% of bed area lost in the last decade) was found at loads of ~30kgN ha^-1 yr^-1, and total disappearance at loads ≥60 kgN ha^-1 yr^-1. Rather than decreased eelgrass growth rates, we observed an exponential decrease in shoot densities and bed area (and subsequentlyareal production) as nitrogen loads increased, suggesting that eelgrass decline in higher-nitrogen estuaries of the Waquoit system occurred largely via lack of recruitment or enhanced mortality of established shoots. Similar to the patterns observed inmany other systems and the experimental results obtained in laboratories or mesocosms, the relationship we observed between nitrogen loads and eelgrass health within the Waquoit system was indirect: increased nitrogen stimulated growth and standing stocksof algal producers, that may have caused severe light limitation of eelgrass. From light budgets that considered water column, epiphyte, and macroalgal shading, we estimated chronic, severe light limitation to newly recruiting shoots in higher-nitrogenestuaries, due mainly to shading by a coexisting ≤15 cm macroalgal canopy. Two management recommendations aimed at eelgrass preservation emerge from this work. First, development and management of watersheds must be conducted such that land-derivednitrogen loading to estuaries is restricted. In the Waquoit Bay estuaries, for example, eelgrass is absent or rapidly disappearing from all but those receiving the lowest (≤15th percentile) loads. Second, shoot density and meadow area, rather than grates per shoot, seem to be adequate variables for routine monitoring of eelgrass health. We also show that the shift from eelgrass- to algae-dominated communities has important consequences for total system primary production and carbon and nitrogencycling. Estimated total primary production by coastal assemblages in the Waquoit Bay system was 135% higher in estuaries receiving relatively high versus low loads of land-derived nitrogen, suggesting important trophic and biogeochemical alterations totemperate estuarine ecosystems as a result of eutrophication.