The river Ayr is the largest river in Ayrshire and contains populations of Salmon (Salmo salar), Brown Trout (Salmo trutta), Grayling (Thymallus thymallus), eel (Anguilla anguilla), Stickleback, Minnow (Phoxinus phoxinus) and Stone Loach (Barbatula barbatula). The river Ayr has one of the largest salmon rod catches, as well as having salmon dwell in tributaries over 300m, the highest point reached by salmon in Ayrshire. Sea Lampreys were recorded by the Ayrshire Rivers Trust in 2004 and it is possible that they are still present in the other Ayrshire rivers.

Loch Doon is the only fresh water body in the South West of Scotland which supports a native population of Arctic Char (Salvelinus alpinus), with several other still waters in the catchment, such as Bogton Loch and Martnaham Loch providing suitable habitat for Perch (Perca fluviatilis) and Pike (Esox lucius).

During the summer months the river Girvan sees a good number of Grey Mullet in the harbor and tidal areas, while the river Stinchar has a large and widespread Eel population.

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