The River Hull valley hosts a variety of wildlife, but much of it is restricted to a small number of protected and managed sites. Much of the Hull Valley was once marsh and rough grazing or "carr" land, the breeding habitats of Snipe and Lapwing, but these have virtually all been drained. Carrs can still be found at Watton, while High Eske Nature Reserve contains an excellent marsh at Pulfin.

Although the headwaters of the River Hull still contain interesting riverine flora and fauna, the man-made reservoirs at Tophill and old gravel pits at Brandesburton and Frodingham are particularly attractive to wildlife.

Over 175 bird species are regularly recorded each year in the valley, together with a variety of mammals including 5 species of bat, and there have been recent sightings of Otter. More than 20 species of butterfly and a dozen dragonfly species are observed annually.

Scarce breeding birds in the valley include Great Crested Grebe, Grey Heron, Shelduck, Little Ringed Plover, Little Owl, Kingfisher, Tree Sparrow and Corn Bunting.

In the upper reaches of the valley, significant numbers of wildfowl winter. All five species of Grebe, seven species of Geese, and seventeen species of duck are regularly seen. The area frequently hosts migrant Garganey and wintering Goldeneye, Smew and Goosander.

The Hull Valley is also a migration route for waders, with Green and Wood Sandpipers, Greenshank, Black-tailed Godwit and Ruff passing through annually. Near the mouth of the River Hull, large numbers of waders including Golden Plover and Curlew can be seen on the mudflats between Paull and Saltend.