The river has been used by some researchers as an indicator of ecological health and is included in the
River Cleddau catchment area's Site of Special Scientific Interest (SSSI) for its wide range of indigenous wild plants and animals, including
water crowfoot,
lamprey and
otter. The Syfynwy is included in the Eastern Cleddau Special Area of Conservation (SAC). In 2009 the Bro Syfynwy Heritage Group were granted £2,750 to produce a leaflet covering rural and historical life around the upper Syfynwy. The Llys y Fran Catchment Project is an ecological study based on the Afon Syfynwy catchment from its source to the Llys y Fran dam. The study, begun in July 2014, is focussed on understanding the blue green algae blooms that have been occurring in the reservoir and, with the support of landowners, will involve soil sampling and nutrient management. The project is being run in collaboration with
Welsh Water and
Natural Resources Wales (NRW). As well as farming, the project will also consider the impact of sewage and forestry on the study area as well as water quality and invertebrate populations. Over the winter of 2013-14 Pembrokeshire Rivers Trust monitored riverflies at Gelli Bridge as part of a wider study of the Eastern Cleddau catchment area. They found fewer numbers than usual, but that most sensitive species were present.
Pollution A pollution incident in 1999 where trade effluent was discharged into the river causing the death of an estimated 1,000 brown trout resulted in a fine of £2,500 and £13,021 costs when the case went to court the following year. ==World War 2==