There is an abundance of flora and fauna at the river. However, as the river flows through urban areas, pollution has long been a problem.
Flora along the river is varied. Bryophytes and algae are common with an abundance of filamentous green algae. Crocosmia, Japanese knotweed and Himalayan balsam are the only invasive species recorded along the river.
The Dodder is home to many water-bird species including mallard, grey heron, kingfisher, dipper, coot, moorhen, grey wagtail, common sandpiper, cormorant and mute swan; the sparrowhawk nests in the trees lining the riverbanks. The red fox is common along the riverbank and the badger and otter have also been seen. In recent years a small feral population of mandarin ducks has become established by the river.
It was reported in 2013 that an Irish Wildlife Trust survey found otters living along the Dodder.
Fish present in the river include brown trout, sea trout, stone loach, three-spined stickleback and European eel. Atlantic salmon can also be found in the river's lower course. Atlantic salmon and lamprey eels are expected to return to most of the river after a more than 200-year absence pending the construction of fish ladders. The Dodder is a popular river for fishing and angling amongst Dubliners. The fishing season is open between 17 March and 30 September.
