We get the feeling that, much like the crocodile from Peter Pan, time is stalking our speaker. "The Nymph's Reply" is full of references to the inevitability of time, seasonal change, and eventual death. The nymph's rejection of the shepherd is based on such references, and she dismantles his argument by distorting his images through the lens of time. It turns out that, a few months down the road, all the shepherd's flowers, fields, and fuzzy sheep don't look nearly as appealing as they did back in April. Tough daffodils for him, then.
In "The Passionate Shepherd" the passing of time is a reason to embrace the delights of the present. Carpe diem! In "The Nymph's Reply," it is the opposite. Carpe nothin'!
"The Nymph's Reply" argues that love, much like nature, decays and become less valuable with the passing of time. Cheery, eh?