The CFES evolved from the Centre for Freshwater Studies, which was founded in 2005.  The first major project undertaken by the centre, the National Source Protection Pilot Project (2005-2010), also commenced in that year.  That project explored options for water source protection in the rural Group Water Scheme sector (small locally managed water provision schemes), a research area that continues to be a focus within the centre.  The centre grew over the following years to include projects on wetlands, agriculture and water quality, carbon cycling in humic catchments, environmental modelling (including climate change impacts) and water policy and provision in the developing world.  It was expanded to include the organic resources research theme in 2012 and was renamed the Centre for Freshwater and Environmental Studies.

The current CFES includes nine academic members, two postdoctoral researchers and eleven postgraduate students.  It engages in inter- and multi-disciplinary research across three main themes: Lake and Catchment Management, Organic Resources Research, and Water and Communities.  The centre also facilitates undergraduate research, and undertakes educational and outreach activities, while providing relevant scientific information for government agencies, policymakers, communities and other interested parties.

Part of the centre's philosophy includes the belief that collaborative studies involving the participation of a number of interested parties add to the effectiveness of research and development.  Within Ireland, CFES is currently undertaking research internally with the Department of Humanities (DkIT), and externally with Teagasc, the Marine Institute, the EPA, the National Federation of Group Water Schemes (NFGWS), University College Dublin, Dublin City University, Monaghan Biosciences Ltd.  and Monaghan Mushrooms Ltd.  It also has strong international research networks, with several international projects funded under Horizon 2020 and the Climate JPI programmes.