Cothill Fen Special Site of Scientific Interest (SSSI) and Special Area of Conservation (SAC) is an alkaline fen system including Cothill National Nature Reserve (The Ruskin Reserve, owned by National Trust managed by Natural England) Parsonage Moor and Lashford Lane Fen managed by Berkshire, Buckinghamshire and Oxon Wildlife Trust (BBOWT).

Cothill Fen is an internationally important wetland site supporting many sensitive freshwater plants and animals and is the largest remaining alkaline fen in Central England. Alkaline fen is a vanishingly scarce habitat these days with most former sites destroyed; the remaining sites are at risk of degradation due to changes in hydrology, inappropriate management or surrounding land-use pressures. In close proximity to Cothill are two other important fen sites; Lashford Lane Fen and Dry Sandford Pit both of which are also BBOWT nature reserves.

Fen habitats develop on permanently water-logged soils with peat forming at the surface. In healthy fen systems water levels typically fluctuate very little with water just at, or just below the surface. In the case of Cothill, the fen is fed by calcareous waters both from the surface and aquifer. Fens are typically low nutrient environments and if appropriately managed and free from pollution, can be exceptional places for freshwater biodiversity.

Cothill Fen is home to a unique assemblage of freshwater life including the northern most population of Southern Damselfly Coenagrion mercuriale, rare Soldier flies, carnivorous plants like Butterwort Pinguicula vulgaris and Bladderwort Utricularia australis, and a primitive group of plants called Stoneworts. Cothill is also home to many locally important populations of plants such as Black Bog-rush Schoenus nigricans, Bog Pimpernel Anagallis tenella, and Marsh Lousewort Pedicularis palustris, all of which are scarce in Oxfordshire.

The Flagship Ponds project has worked with site managers, local experts and volunteers, supporting them in undertaking research into water quality, both within the site and from the surrounding landscape. The work has used citizen science data – collected by local people, to feed into a professional study looking at nutrient pollution and the effects of this on the fen. This work has revealed that nutrient pollution is impacting on the site, something that previous studies have failed to fully recognise. Armed with this new information, techniques to manage nutrients and ameliorate the effects of pollution will be applied and tested on the site.