Restoration is increasingly considered an essential tool to halt and reverse the rapid decline of vital coastal ecosystems dominated by habitat-forming foundation species such as seagrasses. However, two recently discovered pathogens of marine plants, Phytophthora gemini and Halophytophthora sp. Zostera, can seriously hamper restoration efforts by dramatically reducing seed germination. Here, we report on a novel method that strongly reduces Phytophthora and Halophytophthora infection of eelgrass (Zostera marina) seeds. Seeds were stored in seawater with three different copper sulphate concentrations (0.0, 0.2, 2.0 ppm) crossed with three salinities (0.5, 10.0, 25.0 ppt). Next to reducing seed germination, infection significantly affected cotyledon colour: 90% of the germinated infected seeds displayed a brown cotyledon upon germination that did not continue development into the seedling stage, in contrast to only 13% of the germinated non-infected seeds. Copper successfully reduced infection up to 86% and the 0.2 ppm copper sulphate treatment was just as successful as the 2.0 ppm treatment. Infection was completely eliminated at low salinities, but green seed germination was also dramatically lowered by 10 times. We conclude that copper sulphate treatment is a suitable treatment for disinfecting Phytophthora or Halophytophthora infected eelgrass seeds, thereby potentially enhancing seed-based restoration success.