Lyric discussion by seanbrady 

Cover art for Gates to the Garden lyrics by Nick Cave and the Bad Seeds

I think @AlexanderDumbass nailed it. The garden is obviously a cemetery and he visits her there, then he sees her breathing so he knows she is alive, in the next world.

I think the "garden" reference changes in the last verse, to mean the garden of Eden, a metaphor for heaven, where he knows that they will one day meet again.