We propose a new volcanological interpretation of Santorini’s intracaldera fill deposits as revealed by seismic reflection profiles. This interpretation, along with supplementary gravity and geophysical studies, reveals three distinct volcaniclastic units (1–3). From top to bottom these units are attributed to (1) modern infilling sediment, (2) shallow marine phreatomagmatic volcanism associated with the relatively recent formation of the Kameni Islands, and (3) downfaulted ‘Minoan’ pyroclastic deposits, which formed during caldera collapse towards the end of the Bronze Age eruption. Estimates of the volumes of the seismic units and Kameni Islands yield a dense rock equivalent magma volume of 4.85 ± 0.7 km3. The average rate of volcanism over the past c. 3641 years is estimated at 1.3 ×10−3 km3 a−1, and is similar to the rate since the AD 1707 eruption of 1.2 ×10−3 km3 a−1 based on historical lava volume estimates.