In sheltered, eutrophicated estuaries, reduced nitrogen (NHx), and pH levels in the water layer can be greatly enhanced. In laboratory experiments, we studied the interactive effects of NHx, pH, and shoot density on the physiology and survival of eelgrass (Zostera marina). We tested long-term tolerance to NHx at pH 8 in a 5-week experiment. Short-term tolerance was tested for two shoot densities at both pH 8 and 9 in a 5-day experiment. At pH 8, eelgrass accumulated nitrogen as free amino acids when exposed to high loads of NHx, but showed no signs of necrosis. Low shoot density treatments became necrotic within days when exposed to NHx at pH 9. Increased NH3 intrusion and carbon limitation seemed to be the cause of this, as intracellular NHx could no longer be assimilated. Remarkably, experiments with high shoot densities at pH 9 showed hardly any necrosis, as the plants seemed to be able to alleviate the toxic effects of high NHx loads through joint NHx uptake. Our results suggest that NHx toxicity can be important in worldwide observed seagrass mass mortalities. We argue that the mitigating effect of high seagrass biomass on NHx toxicity is a positive feedback mechanism, potentially leading to alternative stable states in field conditions.