The tsunami triggered by the earthquake affected most of the Ionian Sea coast of Sicily, about 230 kilometres (140 mi) in all. The first thing that was noted at all localities affected was a withdrawal of the sea. The strongest effects were concentrated around Augusta, where the initial withdrawal left the harbour dry, followed by a wave of at least 2.4 metres (7.9 ft) height, possibly as much as 8 metres (26 ft), that inundated part of the town. The maximum inundation of about 1.5 kilometres (0.93 mi) was recorded at Mascali.
Tsunami deposits linked to the 1693 tsunami have been found both onshore and offshore. At Ognina, just south of Syracuse, at the head of a ria, a sequence containing several coarse clastic layers has been found, inconsistent with its lagoonal setting. The uppermost coarse layer, which has a strongly erosive base, consists of coarse sand with up to granule size clasts. The layer has been dated as 17th to 18th century based on pottery shards and one well-preserved clay pipe, consistent with the 1693 tsunami. Offshore from Augusta, a sequence identified using chirp sonar data was sampled with a 6.7 metres (22 ft) gravity core in 72 metres (236 ft) of water. Following detailed analysis of both grain size and foraminifera assemblages, eleven possible high-energy events were found based on the presence of large numbers of shallow water forams combined with a greater proportion of fine sand in the same interval. The uppermost two events correlate well with the tsunamis from the 1908 Messina earthquake and the 1693 earthquake.