The haplosporidian parasite Bonamia ostreae is one of the biggest issues facing European native oyster, Ostrea edulis, aquaculture and restoration. Measures to stop the spread of diseases in the United Kingdom have to date relied on the prevention of animal movement from disease positive to disease-free sites. However, these measures are not entirely successful and have seen recurrent failures in recent years, resulting in the gradual spread of B. ostreae across the UK. We tested the utility of protocols for pro-active pathogen diagnostics, combining a portable qPCR machine and field DNA extraction protocols with our experience detecting pathogens in disease challenge systems. We used a stepwise process of overnight incubation, sampling of substrates from the tank system, simplified DNA extraction and rapid diagnostic of the presence of DNA. Here we will present the concept of fully useable system that can be employed on the site of the shellfish farm. The process is now validated against a set of traditional diagnostic techniques including tissue qPCR and histopathology. This rapid, cheap and simple process allows native oyster farmers and restoration practitioners to make proactive decisions on whether to move animals, based on their up-to-date health status, and thus take full control of the risks associated with animal movement.