Only euryhaline fishes were able to recolonize Outer Hebridean fresh waters after the last glaciation so that inland waters now contain only six indigenous, truly freshwater species; salmon, trout, charr, three- and ten-spined stickleback and the freshwater eel. Parts of some lochs are invaded by the sea at stages in the tidal cycle and some 20 species of marine fish may be found at times in inland waters.
Both salmon and sea trout occur in all the larger freshwater systems and sea trout are also found in many of the minor ones.
The original sea trout gave rise to sedentary brown trout populations similar to those of the mainland.
Fluctuations in the Hebridean salmon catch suggest that the stock is affected by the same factors as those affecting Scottish west coast stocks generally: the vast-majority return to fresh water as grilse, while sea trout stocks have been declining over the last 25 years.
Brown trout and eels are almost ubiquitous. Charr occur in Lewis and parts of North Uist but have not been reported from Harris or South Uist and are now only present as sedentary forms. The three-spined stickleback is more widely distributed than the ten-spined.
Outer Hebridean lochs in general have special scientific value because, unlike many Scottish mainland lochs, they have not been affected by the introduction of alien species and some are still in an unexploited state.