For stanza 1, the disobedience of Adam and the immediate cost is documented in Genesis 3:14-24. The full eventual cost, and God’s deliverance, is explained by Paul in Romans 5:12-21.
Stanza 2 refers to the Ark of mercy that rode the flood, a reference to the narrative in Genesis 6:1-8.
Stanza 3’s reference to the “little child” and all that was regained through him is found in Matthew 1 and 2, Luke 2, and a deeper explanation of his significance in John 1.
The “new Jerusalem” referred to in stanza 5 is clarified in Revelation 21.