Land-based eutrophication is often associated with blooms of green macroalgae, resulting in negative impacts on seagrasses. The generality of this interaction has not been studied in upwelling-influenced estuaries where oceanic nutrients dominate seasonally. We conducted an observational and experimental study with Zostera marina L. and ulvoid macroalgae across an estuarine gradient in Coos Bay, Oregon. We found a gradient in mean summer macroalgal biomass from 56.1 gdw 0.25 m −2 at the marine site to 0.3 gdw 0.25 m −2 at the riverine site. Despite large macroalgal blooms at the marine site, eelgrass biomass exhibited no seasonal or interannual declines. Through experimental manipulations, we found that pulsed additions of macroalgae biomass (+4,000 mL) did not affect eelgrass in marine areas, but it had negative effects in riverine areas. In upwelling-influenced estuaries, the negative effects of macroalgal blooms are context dependent, affecting the management of seagrass habitats subject to nutrient inputs from both land and sea.