The Little Danube offers a variety of different types of fish habitat. Common and a number of rare fish species share these waters, including the Danube gudgeon, the Danube ruffe, streber and the European bitterling. Prime sport fishing species include chub, barbel and the prized large catfish.
The waters are also home to a large population of amphibians, the best represented among them green and agile frogs. With a little bit of luck, a green tree frog may be spotted on one of the trees or in nearby vegetation. The Danube crested newt also has suitable habitat along the river.
Birds are the easiest to observe while boating or rafting. Wild duck, Eurasian coot, mute swan and rarely, in particular during migratory periods, wild goose can all be seen on the surface of the water. Grey heron, egret and black cormorant are commonly observed in the surrounding trees. Cormorants select specific trees to gather and roost for the night in large groups. The characteristic nests of the Eurasian penduline tit can also be seen in the crowns of trees.
European beaver activity is evident along the banks of the river as they have expanded their range recently into areas in which beavers were aggressively hunted out of existence at the end of the 19th century. Beavers feed on tree trunk. Their strong teeth are able to cut through and fell even large trees. These fallen trees are used to build beaver lodges and dams and with the fresh branches serving a primary source of food for beavers.The banks of the river are home to the carnivorous river otter and the non-native muskrat.