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.
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.
For this reason Cemlyn has been designated as part of the Ynys Feurig, Cemlyn Bay and The Skerries Special 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.
Other breeding birds found at Cemlyn include black-headed gull, ringed plover, oystercatcher and shelduck.