Biofouling of vessels is implicated as a high risk transfer mechanism of non-indigenous marine species (NIMS). Biofouling on international vessels is managed through stringent border control policies, however, domestic biofouling transfers are managed under different policies and legislative arrangements as they cross internal borders. As comprehensive guidelines are developed and increased compliance of international vessels with ‘clean hull’ expectations increase, vessel movements from port to port will become the focus of biosecurity management. A semi-quantitative port to port biofouling risk assessment is presented that evaluates the presence of known NIMS in the source port and determines the likelihood of transfer based on the NIMS association with biofouling and environmental match between source and receiving ports. This risk assessment method was used to assess the risk profile of a single dredge vessel during three anticipated voyages within Australia, resulting in negligible to low risk outcomes. This finding is contrasted with expectations in the literature, specifically those that suggest slow moving vessels pose a high to extreme risk of transferring NIMS species.