Thirty-two samples of submerged Nautilus macromphalus shells were recovered in 2008 from Lifou, Loyalty Islands in the South Pacific Ocean. Specimens were collected from carbonate-dominated sediment in water depths of 1–3 m. Some specimens were partly buried, whereas others rested on the seafloor. The majority of the specimens (66%) were recovered in a horizontal position, whereas 34% of the specimens were oriented vertically. Some specimens were pristine, with sharp color stripes and little encrustation by algae, cyanobacteria, or epizoans. The majority of specimens have substantial algal and cyanobacterial overcoats with some epizoans. In some specimens, the overcoats also trapped substantial amounts of carbonate sediment. Comparison of the 2008 collection of subtidal specimens to 43 beached Nautilus shells collected in 2002 from the same location reveals that the nearshore taphonomic pathways for drift cephalopod shells can be more complicated than published theoretical models suggest. Nautilus shells may or may not float directly to the beach. Shells not immediately deposited on the beach sink in the shallow water in a vertical position. Weight added by attached organisms and water infiltration, causes the submerged shells to eventually assume a horizontal position. Waves, currents, and bioturbation can then flip the shells over from side to side. Eventually submerged shells are buried, broken apart, or transported onto the beach. Beached shells that follow this taphonomic pathway have conspicuous algal coatings compared to those that simply float to shore. The Lifou subtidal population represents the first substantial modern externally shelled cephalopod collection from a shallow water environment to be analyzed to determine its taphonomic pathways. Conclusions from this analysis can be applied to nearshore deposits that contain externally shelled, fossilized cephalopods.