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Soil frequently occurs as a contaminant on numerous sea, land and air transport pathways. It can carry unwanted invasive species, is widely recognized as a biosecurity risk, and is usually strictly regulated by biosecurity authorities. However, little is known about relative risk levels between pathways, thus authorities have limited capability to identify and target the riskiest soil pathways for management. We conducted a an experiment to test the hypotheses that biosecurity risks from soil organisms will increase both with declining transport duration and with increasing protection from environmental extremes. Soil was collected from two sites, a native forest remnant and an orchard, and stored on, in and under sea containers, or in cupboards, and assayed after 0, 3, 6 and 12 months for bacteria, fungi, nematodes and seeds. Results showed that viability of Pseudomonas spp., bacteria, nematodes and plants declined over 12 months, irrespective of soil source. Also, mortality of most biota was higher when exposed to sunlight, moisture and desiccation than when protected. However, bacterial and fungal numbers were higher in exposed environments, possibly due to ongoing colonization of exposed soil by airborne propagules. The results were consistent with our observations of organisms in soil intercepted from airports and sea ports, and indicated there is potential to rank risks from transported soils based partly on transport duration and environmental exposure. This would help authorities to optimally allocate management resources according to pathway-specific risks.