Separated from the bay by a shingle beach is a brackish lagoon, which is fed by a number of small streams. A weir at the western (Bryn Aber) end of the beach regulates the lagoon's water level.
On islands at the western end of the lagoon, there is an important terncolony, with the only breeding Sandwich terns in Wales. The numbers of breeding Sandwich terns have increased to around 1,500 pairs in recent years, making Cemlyn the third-largest colony in the United Kingdom. Arctic and common terns breed here regularly in smaller numbers but roseate tern now only occasionally. For this reason Cemlyn has been designated as part of the Ynys Feurig, Cemlyn Bay and The SkerriesSpecial Protection Area along with two other nearby sites, Ynys Feurig and The Skerries, and all three are also classed by BirdLife International as an Important Bird Area. Birds interchange regularly between all three sites, and form part of a larger Irish Sea tern population together with birds at sites in Ireland such as Rockabill Island. The tern colony is wardened from May to August.
Cemlyn has attracted a number of vagrant birds. It is famous among twitchers as the site where a bridled tern spent several weeks in July 1988, and where the similarly rare (in a British context) sooty tern was present on and off in July 2005. Both species had at these times been seen by only a very small number of birders in Britain. More recently, a squacco heron was present in June 2015.[2]