ABSTRACT: Climate change intensifies the frequency and intensity of rainfall events, which increases the discharge of freshwater and nutrients to coastal areas. This may lower salinity and increase nutrient availability and, thus, affect estuarine eelgrass populations. We studied the interactive effect of increasing NH₄⁺ levels and low salinity on estuarine eelgrass Zostera marina, grown in microcosm at various combinations of NH₄⁺ enrichment (0, 10 and 25 µM) and salinity (5, 12.5 and 20). Increasing NH₄⁺ had a positive effect on eelgrass performance as long as salinity was kept at ambient level (20). N enrichment was followed by an increase in pigments, photosynthesis and various growth variables and a decrease in stored carbon concentrations (sucrose and starch). Low salinity had an overall negative effect on plant fitness; pigment concentration, photosynthesis and growth were reduced while mortality increased. Exposure to low salinity was also followed by a decrease in sucrose, suggesting that it was used as an osmolyte and/or that photosynthesis could not cover energy requirements needed for osmoregulation or repairing processes. Concomitant exposure to high NH₄⁺ and low salinity turned the positive effect of NH₄⁺ into a strong, negative synergistic effect. Several growth-related variables were affected significantly and mortality increased substantially. We suggest that this simultaneous exposure intensified competition for energy and C skeletons affecting other metabolic processes (e.g. growth, repair processes) negatively. Our results suggest that climate change driven alterations in precipitation and NH₄⁺ loading might seriously impact estuarine eelgrass communities.