For the earth will be filledwith the knowledge of the glory of the Lordas the waters cover the sea.
So two parallels are being constructed: one between the earth and the sea and one between the glory of the Lord and the water. Be careful not to confuse the two. The focus is not that the water fails to cover the entire earth, but rather that the water so completely and so deeply covers the sea.
Also be careful to recognize the time. The focus was not the present but rather the future. This prophet was in the midst of the terror that was the Babylonians. This verse is in the midst of four woes that condemned their actions. He was not speaking from the lofty mountain of success but from the deepest valley of turmoil. The time at which he prophesied was full of uncertainty.
Despite that Habakkuk spoke with absolute certainty about what was to come. That the glory of man is temporary, that the voices of the idols are silent, and that salvation would come from the Lord.
And it is that salvation that will bring glory to the Lord.
Though the fig tree should not blossom,nor fruit be on the vines,the produce of the olive failand the fields yield no food,the flock be cut off from the foldand there be no herd in the stalls,yet I will rejoice in the Lord;I will take joy in the God of my salvation.God, the Lord, is my strength;he makes my feet like the deer's;he makes me tread on my high places.
In the deepest valleys there are even deeper rivers that flow to even deeper seas, none of which are sufficient to hold the glory of our Lord.