The number of alien species transported as stowaways is steadily increasing and new approaches are urgently needed to tackle this emerging invasion pathway. We introduce a general framework for identifying high-risk transport pathways and receiving sites for alien species that are unintentionally transported via goods and services. This approach combines the probability of species arrival at transport hubs with the likelihood that the environment in the new region can sustain populations of that species. We illustrate our approach using a case study of the Asian black-spined toad Duttaphrynus melanostictus in Australia, a species that is of significant biosecurity concern in Australasia, Indonesia, and Madagascar. A correlative model fitted to occurrence data from the native geographic range of D. melanostictus predicted high environmental suitability at locations where the species has established alien populations globally. Applying the model to Australia revealed that transport hubs with the highest numbers of border interceptions and on-shore detections of D. melanostictus were environmentally similar to locations within the species’ native range. Numbers of D. melanostictus interceptions and detections in Australia increased over time, but were unrelated to indices of air and maritime trade volume. Instead, numbers of interceptions and detections were determined by the country of origin of airplanes (Thailand) and ships (Indonesia). Thus, the common assumption that transport pressure is correlated with invasion risk does not hold in all cases. Our work builds on previous efforts to integrate transport pressure data and species distribution models, by jointly modelling the number of intercepted and detected stowaways, while incorporating imperfect detection and the environmental suitability of receiving hubs. The approach presented here can be applied to any system for which historical biosecurity data are available, and provides an efficient means to allocate quarantine and surveillance efforts to reduce the probability of alien species establishment.