The river Kelduá runs through the southern valley of Fljótsdalur, out into the glacier river in Fljótsdalur which makes up the glacier lake of Lagarfljót. The river is rich with brown trout and arctic char. Fishing permits are sold at Hengifoss guesthouse.

Gilsá runs into lake Lagarfljót at the edge of Hallormsstaður forest. Trout from the lake swims up the river mouth which makes an beautiful fishing spot.The national forestry allows fishing in the river, free of charge.

The glacial river that runs through Fljótsdalur, Jökulsá í Fljótsdal, is clear enough for fishing part of the year. Due to the dam build further up the river to form a reservoir to power the hydropower plant in the valley. Fishing permits are sold at the Wilderness center, positioned far up the the northern valley of Fljótsdalur. Fishing poles are also available for rent.