The waters surrounding Yakushima are remarkably clear and rich, with coral reefs, sea turtles, and shoals of tropical fish inhabiting the shallows. The island sits at the boundary between temperate and subtropical oceanic zones, which means biodiversity is high — species typical of both zones overlap here. The best snorkelling spots are on the east and south coasts, where visibility is good and the underwater terrain varied.
Several dive operators run day trips from Miyanoura and Anbo, covering sites ranging from coral gardens to submerged rock pinnacles. Turtles are a common encounter throughout the year, not just during the nesting season. Sea kayaking tours are also available, combining coastal paddling with stops for swimming and snorkelling. Equipment rental is available from operators in Miyanoura; a wetsuit is worth using even in summer given the amount of time you may spend in the water.