An inspection system allows scanning an entire vessel and its contents in a water-filled passage. A radiation source emits a beam of radiation across a radiation path between the radiation source and a radiation detector. An imaging subsystem creates an image of the entire vessel and its contents from the radiation detector, displaying the image for an inspector. If suspect areas are detected, the inspector can flag the vessel for manual inspection. A water exclusion system excludes most of the water from the radiation path, allowing imaging of underwater portions of the vessel in addition to above-water portions of the vessel. A transport system moves the vessel through the passage at a predetermined distance from one side of the passage. Rollers prevent damage to the vessel and the side of the passage in transit, while also positioning the vessel at the predetermined distance from the side of the passage.