The pathogen detection unit which is supposed to detect bacteria and virus particles specific and quantitative on the example organisms E. coli and presumably Salmon pancreas disease virus. The unit consists of three key elements, a microfluidic chip coated with aptamers which are in this case coupled with a FRET system and an optical detection unit. Aptamers are short DNA fragments which specifically recognize their target according to the immune response. The pathogen detection unit is thought to be connected via a bypass to the end-user side constantly monitoring the water quality. Thereby the aptamers will specifically bind their targets which are either virus particles or bacteria. Due to the conformational change during the binding incident a quencher which is coupled to the aptamer will be released. Subsequently the quencher will be out of range of the fluorescent reporter molecule, which is still coupled to the aptamer and a fluorescent signal can be generated, which will be proportional to the amount of target. The pathogen detection unit is supposed to collect valuable data of fish viruses and their infectious doses since these are not known for most fish pathogens.