ABSTRACT: Invasive non-native species (INNS) are expanding their geographic range due to climate change, maritime traffic (primary route) and aquaculture (secondary route), resulting in the potential spread of microbes associated with them. Few studies have investigated the INNS-Pathogen phenomenon. In this study, marine invertebrate species (native and INNS) were sampled monthly over three months and screened by PCR for ostreid herpesvirus-1 microVar (OsHV-1 μVar) and Vibrio bacteria. Both pathogens are negatively associated with bivalve aquaculture. Samples sites included a shipping port, an oyster farm, a marsh nature reserve and a riverine site. Crustacea, Mollusca, Polychaeta, Tunicata and Porifera were sampled. Vibrio spp. were detected in 54.3% (n = 319/588) across all taxa and sample sites. The first detection of Vibrio salmonicida associated with Atlantic salmon Salmo salar was detected in the INNS beaked barnacle Austrominius modestus. OsHV-1 μVar (7.7%, 45/588) was detected in Crustacea, Mollusca and Polychaeta at non-culture sites and in mussels Mytilus spp. at a much lower temperature (average sea surface temperature (SST) 11.25 °C) than previously recorded. The shipping port had the highest Vibrio diversity and OsHV-1 μVar detection. Over half (51.1%) of “recently dead” shore crabs Carcinus maenas had either pathogen detected compared to 29.4% of living crabs. OsHV-1 μVar detection was significantly higher in dead crabs (24.4%) compared to living crabs (5.9%). Findings from this study contribute a better understanding of the role of estuarine native and INNS as vectors/carriers of pathogens, and how the spread of INNS might facilitate the spread of pathogens.