Nature certainly has a big role to play in this poem, and it's not exactly complementary to man's existence. In "The Nymph's Reply," nature is a constant reminder that death is all around us. Nice, huh? Subsequently, the poem becomes a rejection of the pastoral view of the happy-go-lucky countryside put forth by Marlowe's shepherd. Still, Ralegh seems to acknowledge the natural progression from birth to death, but he fails to mention that what is dead rises again the following spring. Slight oversight there, Debbie Downer. His vision of death in nature without new life is, in some ways, just as unrealistic as Marlowe's portrayal of ever-blooming flowers that never wither or decay.
Ralegh's dismal portrayal of nature is a retaliation against the idealized way in which people in the 1600s viewed country life. Just say no!
The withered bed of roses depicted in lines 13 and 15 is not a representation of decay in nature, but an extended metaphor for the inevitable disintegration of romantic love. Sad, and then double-sad.