Survival, metabolism and growth of Zostera marina exposed to hypoxia and sulfides in the water column were examined during a 3-week experiment. Z. marina was collected in the Archipelago of South Fyn, Denmark and kept under controlled laboratory conditions where they were exposed to low oxygen concentrations and two concentrations of sulfides in the water column. Survival of Z. marina was negatively influenced by the presence of sulfides, and photosynthetic activity stopped after 6 days of exposure to high sulfide concentrations (100–1000 μM). Rates of photosynthesis also decreased in plants exposed to hypoxia, but the plants remained alive during the 3-week incubation. Rates of leaf elongation (exposed: 0–13.5 mm mm −1 d −2; control: 24 mm mm −1 d −2) and number of leaves per shoot (exposed: 3.2–4.2; control: 5.1) decreased in all treatments compared to control plants indicating that hypoxia and sulfides have negative impacts on Z. marina metabolism. The non-structural carbohydrate reserves in roots were reduced by up to 81% compared to the controls, whereas the reserves of starch in the rhizomes remained similar to the controls. The exposure to hypoxia and sulfides resulted in loss of above-ground biomass, most severe in the sulfide treatment (55% decrease in shoot:root ratio), suggesting that both parameters may play important roles during die-back events of seagrasses.