The Silurian reefs off Saaremaa in the Baltic Sea were studied by means of high-resolution seismic reflection profiling. The abundance and diversity of the reefs increases off Saaremaa concomitantly with the deepening of the Baltic Silurian Basin towards Gotland. The peak of the reefs around Saaremaa occurred during the Middle Wenlock. The reef facies retreated further off Saaremaa during the Late Wenlock, became episodically restored around the island during the early Ludlow and finally ceased during the late Ludlow. A similar SW–NE–SW migration of reefs reflects an alternating transgressive–regressive pattern in the nearshore shallow shelf environment, where already minor sea-level fluctuations strongly influenced the conditions for reef growth. During the early Wenlock, a bathymetric break with a large barrier-reef-like structure divided the shallow shelf offshore Saaremaa facially into back-reef and southerly sloping fore-reef areas. The width of this SW-migrating barrier (c. 8 km) and the extent of reef bodies within it (c. 4 km) are the largest known in the Baltic region. During the Silurian, the reefs between Saaremaa and Gotland were flourishing to a much larger extent than is visible today. The primary Silurian reef pattern was increasingly destroyed towards Gotland by later erosion. This has resulted in a large area void of Wenlock reefs off northern Gotland. Off southern Gotland, the narrow conical low-energy deeper-water reefs prevail, as the wave-agitated shallow-water facies with larger and lenticular Wenlock and Ludlow reefs are largely eroded around the Gotland Deep.