The meaning of the poem is the idealization of nature and sexuality. Mostly, Marlowe uses natural imagery to underscore his meaning. He mentions shallow rivers, melodious birds, beds of roses, etc., to portray a sense of how natural the relationship between the man and woman is - how much a part of nature.
The allusions used are few and very subtle. The first is the mention of "myrtle". The shepard tells his lady that he shall make her skirt of myrtle, which was the flower associated with the goddess of love and sexuality, Venus. He then underscores this allusion by mentioning "the gods" a few stanzas later. In 16th century England, it would have been more common to reference the Christian God in a poem, but Marlowe references "the gods", which suggests Roman and Greek mythology - as the reference to "myrtle" does.
The only other allusion comes in the reference to May, which historically is the considered as the start of spring (May Day celebrations) and thus the start of the mating period amongst animals. Again, this is a reference to religions more nature based than Christianity, as May Day was originally a Pagan celebration. Marlowe would want his shepard to avoid Christianity as to avoid the morality questions imposed upon sexuality by Christian teachings.