The theme of this last Hopkins poem, written in the form of a Petrarchan sonnet, is the questioning of God's justice. Hopkin's precedes the actual sonnet by quoting, in Latin, from Psalm 19, "Righteous art thou, O Lord, and upright are thy judgments."

Nevertheless, the poem begins by raising doubts about this notion of God's righteousness. It asks, if you are a just God, why do sinners prosper and yet my own work seemingly amounts to nothing? The larger theme explored is why do the evil thrive while the good people suffer?

Hopkins questions why "birds breed" (accomplish, create) but he cannot accomplish anything. He calls himself "Time’s eunuch." A eunuch was a castrated male who could not beget children—Hopkins says that time has castrated him so he can accomplish nothing. The poem is a cry from the soul, asking God for help.

Hopkins was a priest and here laments that he has given his life over to God and wants to do good, but feels he has wasted his time. He ends by imploring God to send his "roots rain" so he can accomplish the good work that wells up inside him.

The primary theme of Victorian poet Gerard Manley Hopkins's "Thou art indeed just, Lord" is the philosophical problem of evil.

This issue concerns the existence of evil in a world thought to be governed by an all-powerful and benevolent god. The poem's epigraph, or the short passage in Latin that precedes the poem, comes from the opening lines of Jeremiah 12: "You are always righteous, Lord, when I bring a case before you. Yet I would speak with you about your justice: Why does the way of the wicked prosper?" (Jeremiah 12:1 NIV). Hopkins echoes this sentiment in his poem's opening lines: "Thou art indeed just, Lord, if I contend / With thee; but, sir, so what I plead is just. / Why do sinners’ ways prosper?" (1-3). He claims that God is "just," or that he rewards the good and punishes the bad, but is troubled by the fact that God seems to at times reward the bad as well. Though God is just, he allows sinners to prosper. With this, Hopkins evokes the problem of evil.

The poem's second theme is humans' relationship to God. Like Job in his discussion with God in the whirlwind, the persona gives up attempting to make sense of the problem of evil and merely asks for God's favor. The poem's last line reveals this change: "Mine, O thou lord of life, send my roots rain" (14). Hopkins here uses roots and rain as an analogy for the relationship between humans and God: like how plants require rain to survive, humans require God's grace. With this, Hopkins suggests that humans cannot come to a conclusion about God's actions in moral concerns, and that all humans can do about the problem of evil is ask for God's compassion.

Please explore eNotes's guides to Gerard Manley Hopkins and analyzing poetry linked below for more information!

Gerard Manley Hopkins’ poem, “Thou Art Indeed Just …” is one of what are called the “terrible sonnets”, a group of poems in which Hopkins struggles with problems of religious doubt. An Anglican who converted to Roman Catholicism and joined the Jesuit order, Hopkins was deeply unhappy with his work in Ireland, and assailed by doubts about his faith. In this poem, Hopkins is concerned with the issue of theodicy, the justice of God, and the question of why there seem to be no immediate rewards for goodness and punishments for evil.

Also, the beauty of nature is contrasted with fallen humanity in the poem.