An understanding of undesirable disturbance to the balance of organisms is needed to diagnose marine eutrophication as defined by EU Directives and OSPAR. This review summarizes the findings of the UK Defra-funded Undesirable Disturbance Study Team, which concluded that ‘an undesirable disturbance is a perturbation of a marine ecosystem that appreciably degrades the health or threatens the sustainable human use of that ecosystem’. A methodology is proposed for detecting disturbance of temperate salt-water communities dominated by phytoplanktonic or phytobenthic primary producers. It relies on monitoring indicators of ecosystem structure and vigour, which are components of health. Undesirable disturbance can be diagnosed by accumulating evidence of ecohydrodynamic type-specific changes in: (i) bulk indicators; (ii) frequency statistics; (iii) flux measurements; (iv) structural indicators; and (v) indicator species. These are exemplified by (i) chlorophyll, transparency, dissolved oxygen, and opportunistic seaweed cover; (ii) HABs frequency; (iii) primary production; (iv) benthic and planktonic ‘trophic indices’; (v) seagrasses and Nephrops norvegicus. Ecological Quality Objectives are proposed for some of these. Linking the diagnosis to eutrophication requires correlation of changes with nutrient enrichment. The methodology, which requires the development of a plankton community index and emphasizes the importance of primary production as an indicator of vigour, can be harmonized with the EU Water Framework Directive and OSPAR’s Strategy to Combat Eutrophication.