Seagrasses have declined in many places around the world, and the Swedish Skagerrak coast is no exception. Between the 1980s and 2000, the cover of eelgrass (Zostera marina L.) on the Swedish Skagerrak coast decreased about 60%. In the present study, the sites that were investigated in the 1980s and 2000 were revisited (1655 ha) in 2003 and 2004 to investigate long and short term temporal and spatial differences in eelgrass coverage. The distribution of eelgrass was mapped from a small boat using an aquascope and a GPS receiver. No variation in total (about 150 km) or regional (about 20 km) eelgrass cover was found between 2000 and 2004, but there were substantial changes (both losses and gains) in meadow size on a local (less than about 2 km) scale. The results have implications for management of shallow soft bottoms, particularly because it was shown that even though no eelgrass is found in a single survey in a specific area, there could be eelgrass growing there in the following years.