What does Psalm 139:6 mean?

David was overwhelmed by the Lord's omniscience. Such knowledge lay beyond his comprehension. He said it is "too wonderful," meaning extraordinary or surpassing one's ability to grasp.

In Romans 11:33–34 the apostle Paul wrote: "Oh, the depth of the riches and wisdom and knowledge of God! How unsearchable are his judgments and how inscrutable his ways! For who has known the mind of the Lord, or who has been his counselor?" God's wisdom and knowledge are beyond our ability to comprehend (Isaiah 55:8–9). It is futile to try to figure out such mysteries as the blending of His election and our human responsibility to believe the gospel. It is best to leave incomprehensible matters in the hands of God, whose knowledge is too wonderful to attain (Deuteronomy 29:29). It is also impossible to know how God can transform sinners into saints, but He does so and never fails in the process (Philippians 1:6; 2:13).

That doesn't mean we can't know anything about God. Nor does it mean God wants us to ignore reason in favor of emotion or naivety (Acts 17:11; Matthew 10:16). Scripture upholds the virtues of wisdom, learning, and clear thinking (Proverbs 3:13–15; Colossians 2:8). It encourages us to know what we can, and learn what we're able (2 Timothy 2:15), without pretending we can know everything.