When You Don’t Understand What God Is Doing: Pray, Remember, Rejoice

Three biblical responses to uncertainty, fear, and difficult circumstances from Habakkuk 3.

Have you ever prayed about something, desperately wanted an answer from God, and then struggled when things didn’t turn out the way you hoped?

Maybe you were praying for healing, financial provision, restoration in a relationship, or simply some peace in the middle of an overwhelming situation.

You believe God is good. You believe He is sovereign. But you still find yourself asking, “Lord, what are You doing?”

If you’ve ever felt that way, you’re not alone.

The prophet Habakkuk knew what it was like to wrestle with difficult questions about God’s purposes. He lived in a time of tremendous uncertainty, when the world around him seemed to be falling apart.

But Habakkuk’s struggle wasn’t simply about difficult circumstances. He was witnessing a nation turning away from God, and he knew something was terribly wrong.

His journey teaches us three important responses when life doesn’t make sense.

When God’s Answer Isn’t What We Expected

Habakkuk lived during a deeply troubling time in Judah’s history.

God’s people had turned away from Him. Wickedness, violence, corruption, and injustice had become widespread. Those who should have upheld righteousness were neglecting it, and the vulnerable were suffering.

Habakkuk saw what was happening and cried out to God.

In Habakkuk 1:2–4, he questioned how long God would allow violence and injustice to continue.

Where was God? Why wasn’t He doing something?

But God wasn’t silent. He was working.

And His answer was not what Habakkuk expected.

God revealed that He would raise up the Babylonians, a powerful and wicked nation, to bring judgment upon Judah.

Judgment was coming because God’s people had turned away from Him.

Their sin mattered. Their rejection of God’s ways mattered. Their injustice and wickedness would not simply be overlooked.

Yet Habakkuk struggled with God’s answer.

How could a holy and righteous God use a nation even more wicked than Judah to accomplish His purposes?

It was a difficult question, and Habakkuk didn’t pretend otherwise.

God’s response revealed that His purposes would come to pass at the appointed time. Babylon’s wickedness would not escape judgment either. God remained sovereign over both nations.

Habakkuk had to learn something we still need to understand today:

We may not understand everything God is doing, but we can trust who He is.

God is holy. He is just. He is merciful. And He has not lost control.

This doesn’t mean every hardship we experience is God’s punishment for a particular sin. Habakkuk was dealing with a specific judgment God had revealed against Judah. But his account reminds us that sin is serious, God’s justice is real, and His purposes cannot be defeated.

That brings us to Habakkuk chapter 3.

1. Pray: Bring Your Questions to God

In Habakkuk 3:1–2, the prophet responds to God’s revelation with prayer.

He is afraid. He knows difficult days are coming. He doesn’t fully understand why God has chosen to act this way.

But rather than turning away from God, he turns toward Him.

In the middle of his prayer, Habakkuk makes a remarkable request:

“In wrath remember mercy.” Habakkuk 3:2 (KJV)

Think about what he is asking.

Habakkuk recognizes that God is righteous in His judgment. He doesn’t ask God to pretend Judah’s sin doesn’t matter. Instead, he pleads for mercy in the midst of judgment.

He knows that God is both just and compassionate.

That is an important lesson for us.

Faith doesn’t mean pretending we have no questions. Faith means bringing our questions to the God we trust.

Sometimes we allow fear, frustration, and disappointment to consume our thoughts. We focus so intently on what is going wrong that we forget where to turn.

Habakkuk shows us another way.

When I don’t understand what’s happening, I can talk to God.

We can approach Him honestly, reverently, and with confidence in His character.

And we should come with humble hearts, recognizing that we, too, are sinners who need God’s mercy.

Prayer isn’t about convincing God to follow our plans. It is about bringing ourselves before Him, acknowledging who He is, and learning to trust His purposes even when we don’t understand them.

2. Remember: Look Back at God’s Faithfulness

After praying, Habakkuk begins remembering the mighty works of God.

In Habakkuk 3:3–15, he describes God’s overwhelming power and glory through vivid poetic imagery.

He speaks of mountains trembling, waters responding to God’s authority, and nations standing before His power.

These images recall God’s mighty acts in the history of Israel.

Consider what God had done for His people.

The Israelites had suffered under the oppression of Egypt. Pharaoh had enslaved them, and their suffering was great.

But God had not forgotten His people or His promises.

He heard their cries, remembered His covenant, and delivered them through His mighty power.

He brought them out of Egypt, led them through the wilderness, and revealed His glory at Mount Sinai.

The God who delivered Israel was the same God Habakkuk was crying out to.

And that God had not changed.

The Babylonians might be powerful, but they were not all-powerful.

God ruled over nations, creation, and history itself.

The size of our problems does not change the greatness of our God.

When we’re overwhelmed by circumstances, we can lose sight of that truth.

Our problems become so large in our minds that we begin measuring God’s ability against the size of our difficulties.

But Habakkuk reminds us to look backward and remember God’s faithfulness.

Remember His promises. Remember His mighty works. Remember His mercy toward those who call upon Him.

And remember that God’s power is never separated from His holiness.

The God who delivered Israel from oppression is also the God who would judge Judah for its sin.

He is neither indifferent to wickedness nor powerless to save.

That brings us to an even greater reason to remember His faithfulness.

We can look back beyond Egypt and beyond Habakkuk to the cross of Jesus Christ.

There we see God’s holiness, justice, love, and mercy revealed in His provision of salvation for sinners.

God has not left us without hope.

3. Rejoice: Find Your Strength in God

Perhaps the most remarkable part of Habakkuk’s story comes at the end.

In Habakkuk 3:16, the prophet is still trembling.

He knows trouble is approaching. His body responds with fear. His circumstances have not suddenly become comfortable.

Habakkuk has prayed. He has remembered God’s mighty works. But the difficult future remains.

Then he describes what may lie ahead.

The fig trees may not blossom. The vines may produce no fruit. The fields may yield no food. The flocks and herds may disappear.

For Habakkuk’s people, these weren’t minor inconveniences. They represented the possible loss of the very things they depended upon for survival.

And yet, in the face of all that uncertainty, Habakkuk declares:

“Yet I will rejoice in the LORD, I will joy in the God of my salvation.” Habakkuk 3:18 (KJV)

Notice what hasn’t changed.

The danger hasn’t disappeared.

The future hasn’t become certain.

His fear hasn’t vanished.

But Habakkuk chooses to rejoice in God.

His joy is not based on whether his circumstances turn out as he desires.

His joy is rooted in the God of his salvation.

This is not a call to ignore pain or pretend suffering doesn’t hurt.

Genuine faith doesn’t mean fear always disappears. Habakkuk was still trembling.

But he had learned where to place his confidence.

In Habakkuk 3:19, he declares that the Lord God is his strength.

Not his resources. Not his ability to control the future. Not his understanding of every detail.

The Lord Himself is his strength.

And because of that, he could rejoice even when everything around him seemed uncertain.

Our Greatest Need: God’s Mercy and Salvation

There is something important we must not overlook in Habakkuk’s story.

Judgment was coming upon Judah because of sin.

God had shown tremendous patience toward His people, but their persistent wickedness and rebellion could not be ignored forever.

That should cause each of us to consider our own standing before a holy God.

Scripture teaches that all of us have sinned and fallen short of God’s glory (Romans 3:23).

We may look at the wickedness around us and recognize how far the world has wandered from God. But the problem of sin isn’t confined to a particular nation, generation, or group of people.

It is a problem within every human heart.

And just as God’s judgment against Judah was real, Scripture warns that a final judgment is coming when every person will give an account before God.

That is a sobering truth.

But it is not where the story ends.

Remember Habakkuk’s plea: “In wrath remember mercy.”

As Christians, we have the privilege of seeing the fullest revelation of God’s saving mercy in Jesus Christ.

God did not ignore our sin. He provided the way for sinners to be forgiven and reconciled to Him.

Jesus Christ, the sinless Son of God, came into the world, lived a perfect life, and willingly died on the cross for sinners.

He bore the punishment for sin, was buried, and rose again on the third day.

Through His death and resurrection, God has provided salvation for all who repent and put their faith in Jesus Christ.

Romans 5:9 teaches that those justified by Christ’s blood will be saved from God’s wrath through Him.

The greatest rescue we need is not simply deliverance from difficult circumstances. It is deliverance from sin and the judgment we deserve.

And that rescue is found in Jesus Christ alone.

We cannot earn it by being good enough, attending church, or trying to balance our wrongs with good deeds.

Salvation is God’s gift of grace, received through faith in Jesus Christ (Ephesians 2:8–9).

If you have never trusted Christ, don’t overlook the mercy God offers through Him.

The most important question isn’t whether all your circumstances will improve tomorrow.

It is whether you have been reconciled to God through His Son.

And for those who have trusted Christ, this salvation gives us a reason to rejoice that reaches far beyond our present circumstances.

Our hope is not that life will always be easy.

Our hope is that Jesus Christ died, rose again, and has secured salvation for His people.

Putting It Into Practice Today

Whatever you’re facing today, consider these three simple responses.

You don’t have to understand everything God is doing to trust Him.

You don’t have to see how every difficulty will be resolved before you can rest in His faithfulness.

And you don’t have to have every fear disappear before you can find joy in Him.

Habakkuk learned that even when judgment was approaching, even when the future was frightening, and even when everything he depended upon might fail, the Lord remained his strength.

The same God remains sovereign today.

And through Jesus Christ, He offers the mercy and salvation we so desperately need.