Unique natural characteristics were the reason for designating Mali Ston Bay a protected area in 1983. In 1998, the protection status of Mali Ston Bay was changed to a strict reserve and in 2002 it was declared a protected special marine reserve.

Mali Ston Bay has a stable ecosystem with ideal conditions for the development of mariculture. It is especially important to preserve its surrounding area because the bay cannot tolerate any human consequences or pollution. Mali Ston Bay is one of the last locations in Europe where the sea quality is graded with an A mark, which allows consumption directly from the sea.