The Blackwater - The river that runs through Cork, Jimmy McCarthy's home town.
A "geek" (not Greek), is a term used to denote a freak, misfit, etc., and of course alchemy is the pseduscientific study of converting base metals into gold.

It is said that unless you totally give up preconceptions and mental addictions, stop fighting them in other words, and walk away from your "old life" and your emotional baggage, you will never be able to experience freedom.
But once you do, they say, you will feel the hand of the creator.

One also has to look at the selective repetition of the last refrain, and compare Jimmy's comparisons and connections in regards to the theme.

Every time I sing it, the hairs stand up on the back of my neck.

Breandán