The poem presents a "dialog" between Spense and his lady. He attempts to immortalize her by writing her name in the sand, but the waves (time) relentlessly erase what he writes. He writes again, with the same results.
The poem them switches to his lady who tells him that he is foolish to attempt to make immortal that which is temporal; she will pass just as the writing in the sand.
Spenser then reenters the conversation and tell her that although there is a physical/temportal part to her nature, his verse will make her immortal.
He summarizes the theme in the final couplet: although things physical may perish, the spiritual nature of their love will transcend death and even grow.