Seagrasses belong to the most productive ecosystems in the world. Although they only cover a very small part of the world’s oceans, they store immense amounts of carbon every year and thus, are of high ecological importance. However, seagrass productivity, and photosynthesis in particular, can be impacted by several stressors such as marine heatwaves and decreasing water qualities arising from river run-off and high nutrient loading (eutrophication and sediment stress). Information about the molecular physiological response of seagrasses to such abiotic stressors is still sparse. I will address this knowledge gap by applying novel molecular biomarker techniques such as metabolomics and proteomics on seagrasses present in Shark Bay, Western Australia, and the Swan-Canning estuary in Perth. The application of ‘omics’ techniques can reveal in depth and ‘hidden’ stress responses as they allow a targeted early detection of physiological changes, and are thus proposed to be of high value for both seagrass management and conservation.