When clinical disease in fish is discovered in production facilities, the fish are usually already very sick. When possible, treatment is initiated immediately , but decreased welfare , increased mortality and economic loss is nevertheless often a consequence . Therefore, prophylaxis and early detection of pathogens could present facility managers with the possibility to intervene prior to clinical outcome and severe disease . We have developed a non-invasive Fluidigm chip tool based on environmental DNA/RNA (collectively eNA ) from water samples for early detection and surveillance of 11 pathogens relevant for Danish aquaculture. For three of the diseases, controlled experiments have been conducted correlating the eNA levels in the water with the disease status in the fish. Common for these experiments were that eNA revealed an elevation of the disease-causing organisms before clinical signs appeared , enabling early intervention before fish show clinical signs of disease (Fig. 1). Our tool can therefore be used to detect pathogens in the early phase, before disease becomes severe, facilitating interventions to limit disease and increase the welfare of the fish, which is a requirement for sustainable animal production.