The lake is naturally populated by
brown trout whose native stocks became depleted in the latter half of the 20th century; at peak, there were 100,000 to 120,000 brown trout in the lake. Nutrient loading, notably of phosphorus, originating from intensive agricultural developments upstream caused a progressive enrichment of the Lough's waters which led to a substantial decrease in the number of trout from the 1970s to the early 2000s.
Zebra mussels, an invasive species, were first seen in the lake in 2000 and there followed a huge increase in their population. A state agency,
Inland Fisheries Ireland, monitors the water quality, including the level of phosphorus, and in conjunction with local organisations, primarily the Lough Sheelin Trout Preservation Association, it and a predecessor body, the Inland Fisheries Trust, has stocked the lake with farm-reared trout. There is also an abundance of
common roach in the lake, and other species present include 3- and 9-spined stickleback, pike, perch, and eels. ==Status==