"The Day is Done" isn't really a "nature" poem. Longfellow doesn't go on for pages about bunnies or sheep or waterfalls or hillsides. Still, check out all the images in this poem that come from the natural world. Even when a poem is about sitting inside and reading, the natural world is still a really important source of poetic imagery. We think of the natural world as sort of hanging out in the background in this poem, giving it extra texture and richness.
Images of nature are a subtle, calm presence in this poem, helping to create the peaceful, rhythmic feeling of the text.
The natural imagery in "The Day is Done" is mostly nonspecific and clichéd. It provides a general "poetic" feeling without contributing much to the meaning or impact of the poem.