A major bottle-neck for eelgrass (Zostera marina) re-colonization is seedling survival and patch establishment as mortality rates among the young seedlings are high even in areas where light conditions and physical exposure should support survival. Since little is known about the reasons for the mortality we here focus on the potential negative impact of macroalgal mats on seedling growth and survival. The high productivity of these fast-growing algae results in large diurnal variations in the oxygen concentrations within the mats and the lower parts may experience prolonged periods of anoxia. For eelgrass even short periods of water column anoxia may have severe implications for growth and survival. In addition, excessive covering by macroalgal mats decrease the available light at leaf surface and may hamper the diffusive movement of oxygen, inorganic carbon and nutrients to and from the shoot thus further impairing growth and survival. Our objectives were to assess the impact of algal mat thickness on seedling performance. A laboratory experiment was set up early in summers 2009 and 2010 using a 2-factorial design. Eelgrass seedlings were grown under three levels of algae and with two types of mats: Chaetomorpha linum and artificial macroalgae. The two types of mats were used to separate physical and metabolic effects of algal presence. During the growth period concentrations of oxygen and sulphide and their diurnal variations in the mats were measured using microelectrodes.