Perkinsus marinus and Haplosporidium nelsoni are the main active pathogens causing Dermo and MSX, respectively, in wild and farmed eastern oysters (Crassostrea virginica) of Great Bay, NH. In this study, quantitative competitive PCR (QCPCR) was used to simultaneously detect and quantify both organisms in the water column and individual oysters of Great Bay Estuary. QCPCR requires co-amplification with a known quantity of competitor DNA, which shares most of the nucleotide sequence with the target DNA. Due to the known ratios of competitor and target, it allows for precise quantification of DNA present in samples. This study found both organisms were present in estuarine waters at three Great Bay sampling sites throughout the “typical oyster season,” or when oysters are most active and spawning (June through November). Results also showed that both pathogens exhibited an oyster-effect, whereby pathogenic DNAs were more frequent and variable in water associated with oyster habitats than a non-oyster associated control site. This finding enhances understanding of disease-causing mechanisms of those organisms in New England estuaries and allows insight into where best to site oyster restoration areas. Combined with previous study of the consistency between the QCPCR and histological results of diseased oysters, the study also demonstrates accurate detection and quantification of oyster pathogens in both environmental and individual oyster samples.