The large western Irish lakes are natural salmonid lakes and a unique ecological resource. Lough Mask (82 km(2)) and Lough Conn (50 km(2)), Co. Mayo, are among the finest, natural, wild brown trout fisheries in Europe. Recently, however, threats have arisen to water quality in Lough Conn as a result of agricultural intensification. A doubling of phosphorus (P) inputs to Lough Conn for the period 1980 to 1990 caused a number of ecological changes such as an apparent increase in littoral algal production; while arctic charr (Salvelinus alpinus L.) have also disappeared from the lake over the same period of time. The changes in Lough Conn appear to represent an early phase in the eutrophication process. The western Irish lakes represent a super-sensitive ecological category requiring particularly strict catchment controls in order to protect the diversity of native flora and fauna including unusual glacial relict species and the unique genetic strains of fish which are present. Catchment management committees were established in order to study and reverse the perceived early-stage eutrophication problem in Lough Conn and in order to prevent the occurrence of similar problems in the case of Lough Mask. These committees have a sectoral basis covering: agriculture, local authority functions (sewage, rural septic tanks, planning and environmental control), forestry, peat harvesting and drainage works, as well as having representation from the fisheries boards and the Environmental Protection Agency (EPA). Management of these relatively pristine lakes is perhaps a more difficult problem than that of cleaning up an obviously degraded resource. This is especially so since they are located in regions which are economically underdeveloped and where a real need exists to improve economic returns from farming, tourism and industry in the catchments. The importance of developing a sustainable, ecologically-based management strategy which will maintain existing high quality lakes into the next century with their irreplaceable genetic and ecological resources intact cannot be over-emphasised. The challenge is to devise refined management strategies which will eliminate nutrient wastage to waters and yet allow an appropriate level of sustainable development in the area. The management of Lough Conn and Lough Mask is described in some detail concentrating in particular on the efforts to reduce phosphorus loss from agriculture in the catchment but also emphasising the importance of a multi-sectoral approach to phosphorus load reduction.