There are many important salmon and sea trout rivers within the area. The Lower Bann connects Lough Neagh to the sea and drains over 1/3 of Northern Ireland. The river is navigable but has also importance for game and coarse fish. The Lower Bann is noted for salmon but also supports healthy populations of roach, pike and other coarse fish. The river also supports a freshwater eel fishery at Toomebridge just outside the area which has great commercial importance. Other important salmon and sea Trout rivers include the Bush and the Roe. The Bush is home to the Department of Agriculture's Salmon research station. The spate rivers of the Glens of Antrim also support healthy stocks of brown trout, sea trout and salmon. There are direct relationships between the length and intensity of spate and the management of the upland blanket bog areas. In addition rivers such as the Maine, Sixmilewater and the Braid support runs of 'Dollaghan' a big lake trout unique to Lough Neagh which run these rivers to spawn. All wetland areas require special management.
Many parts of the upland area, particularly parts of the Garron Plateau near Carnlough, are peppered with small lakes all of which provide important habitats for birds, fish and insects. Lough Begg on the River Bann has international importance for bird life. There are also several important reservoirs within the region including Woodburn, Killyglen, Quoile and Altnahinch. All water courses have importance for insect and plant life and support rich habitats including birds such as the heron, dipper, grey wagtail and many different species of bats. Increasingly otters are becoming more common within some of the water systems within the area.