Two methods of assessing the risk of species introduction by ballast water are discussed, species-specific and environmental similarity assessments, each for alignment with four proposed principles of risk-based resource management: (i) society accepts that low risk scenarios exist; (ii) risk assessment is capable of identifying low risk scenarios; (iii) risk mitigation strategies exist; and (iv) mitigation costs are less than the cost of performing risk assessment. All four principles were met in some circumstances for both methods. Species-specific ballast water risk assessment is best suited to situations where the assessment can be restricted to a limited set of harmful species on journeys within bioregions where ballast water is a small component of natural genetic exchange.Environmental similarity risk assessment is appropriate for journeys that start and end in locations which have very little or no natural genetic exchange, such as journeys between non-contiguous bioregions. Because a large number of species are not assessed individually, environmental match assessments necessarily will be restricted to fundamental variables such as temperature and salinity. A number of bioregion classifications have been identified in the world’s oceans, some of which at a scale that may be appropriate for ballast water management. The suitability of any particular classification, however, needs further examination.