We conducted geophysical surveys on Beacon Island in the Houtman Abrolhos archipelago offshore Western Australia, to investigate areas of archaeological interest related to the 1629 Batavia shipwreck, mutiny, and massacre. We used three complementary near-surface geophysical survey techniques (total magnetic intensity, electromagnetic induction mapping, and ground-penetrating radar) to identify anomalous target zones for archaeological excavation. Interpreting near-surface geophysical anomalies is often complex and nonunique, although it can be significantly improved by achieving a better understanding of site-specific factors including background conditions, natural variability, detectability limits, and the geophysical response to, and spatial resolution of, buried targets. These factors were not well-understood for Beacon Island nor indeed for the Australian coastal environment. We have evaluated the results of controlled experiments in which we bury known targets at representative depths and analyze the geophysical responses in terms of an ability to detect and resolve targets from natural background variability. The maximum depth of detectability of calibration targets on Beacon Island is limited to approximately 0.5 m due to significant variations in background physical properties between a thin () and highly unconsolidated dry sand, shell, and coral layer of variable thickness overlying a sea-water-saturated sandy half-space. Our controlled measurements have implications for calibrating and quantifying the interpretation of geophysical anomalies in areas of archaeological interest, particularly in coastal and sandy-coral island environments. Our geophysical analyzes contributed to the discovery of archaeological materials and five historical burials associated with the 1629 Batavia shipwreck.