Aquifer-fed naturally fluctuating water bodies are temporary lakes, called turloughs and found in areas of carboniferous limestone. Turloughs have no visible inlet or outlet streams but are fed from groundwater. They are unique environments both in terms of the geology and the rare wildlife which they support. As they are fed from groundwater they regularly fill with water in winter and empty in the summer. In Carmarthenshire Pant-y-Llyn turlough can be found at the eastern end of Carmel Woods SAC and is the only example of a turlough in Wales. It is usually empty by June–July and fills again from October to December.

Because of the periodic filling with water vegetation is zoned around the turlough specialist plants can be found here that can live with variations in flooding. There is a clear sequence of moss, swamp plants and woody plant communities, which occupy different zones in the basin.

The turlough may not look that dramatic, despite its uniqueness in the country, but it is the habitat of a number of rare and highly specialised species.  A minute species of moss has been identified there called Ephemerum hibernicum, which was confirmed at the time as the first non-Irish record of this species.  It has subsequently been found by a reservoir in Monmouthshire and a lake in Portugal, but is otherwise restricted to a few sites in Ireland.  It needs fluctuating water levels and lime-rich mud on which to grow, making Pant-y-llyn an ideal site for it.  Despite its tiny size, there is little doubt that E. hibernicum is an extremely rare species - probably one of the rarest in Carmarthenshire. 

The lake also holds one of three known Carmarthenshire populations of Aphanorrhegma (Physcomitrella) patens.  This is another small, subtle moss that appears in late summer on neutral or lime-rich ground that has been flooded earlier in the season.  It grows and produces spores in a matter of weeks, which has made it a perfect experimental organism for scientists.  As a result, Aphanorrhegma is the most intensively studied of all moss species.  A few plants from the Pant-y-llyn population were collected in 2005 and are being grown by scientists from Leeds University, who are studying DNA variation within the species.

The other bryophyte of interest at Pant-y-llyn is the large aquatic moss Fontinalis antipyretica, which grows in great hanging masses from overhanging trees that are flooded in winter but exposed in summer.  Fontinalis is a common moss on Carmarthenshire's rivers, but is known from very few lakes in the county.  Its habit of hanging from tree branches is also characteristic of turloughs in Ireland.

There is also a good range in aquatic invertebrates, including aquatic beetles and freshwater crustacean.

In the past Pant-y-llyn has been threatened by nearby quarrying activities but has been protected by inclusion in the National Nature Reserve. Today it remains vulnerable to actions that may alter the hydrology or water quality.

The turlough is surveyed and monitored by CCW. The site’s uniqueness makes it very important that its characteristic ecology and hydrology is maintained.