In stanza 5, what does the word "it" refer to?

There are only four stanzas in this poem by William Blake, so I think you are actually referring to the word "it" in line five, rather than stanza five. The article "it" here refers back to the "wrath" mentioned in the previous line, which the speaker did not express and which, therefore, grew. However, this poem is an extended metaphor, as the title suggests, in which wrath is imagined taking the physical form of a tree—indeed, a "poison tree," as Blake labels it. The speaker "waters" this wrath, in its tree-like form, and, like a tree, it grows, but the water the speaker provides it with is comprised of his fears, tears, and deceit. The metaphorical tree of wrath thrives on, and is nurtured by, the speaker's bad feelings toward his "foe" and his inability to simply confess his feelings and therefore purge them. Instead, the wrath grows until it bears fruit, which kills the speaker's foe.