We report the discovery and identification of five ancient stone artefacts associated with a submerged freshwater spring at the underwater archaeological site WH1 in Murujuga (Dampier Archipelago), Western Australia. A limiting date applied to the site based on timing of inundation suggests it was occupied in the Late Pleistocene or Early Holocene. The site is situated well below the intertidal zone having been recorded at 14 m depth in Flying Foam Passage. This discovery highlights the high potential of these submerged springs as archaeological survey targets. We discuss results of a recent survey that expands the number of confirmed artefacts located at WH1 and the geomorphological context in a large calcareous depression associated with a freshwater source. This study demonstrates how submerged landscape research using a suite of technologies can reveal archaeological assemblages in this tropical geomorphological environment, and that adapted techniques could be applied to other tropical conditions such as mangrove coasts, large deltaic plains, or reef-building environments. There are likely thousands of drowned archaeological sites on the continental shelf of the tropics, extending from the intertidal zone to the lowest point of the culturally occupied landmass, at approximately 130 m below modern sea level.