In the third stanza of this poem, Arnold creates a metaphor through the phrase "the Sea of Faith." Here, Arnold is comparing the sea to the strong religious feelings which the people of England once held.
The effect of this metaphor is to reinforce Arnold's central message: that people were once strong in their religious beliefs but that, thanks to the rise of scientific thinking and discovery, the nation's faith has been weakened. In other words, people now question the ideas that they once held true.
To demonstrate this decline of faith, Arnold talks about the "melancholy, long, withdrawing roar" of the sea. So, just as the tide ebbs and retreats, faith has also disappeared from view. The effect of this is to create a somber and depressing mood. By using the word "melancholy," for example, Arnold expresses his sadness at this development.
Arnold therefore mourns the decline of religious belief, and the metaphor of the "Sea of Faith" is instrumental in helping him to express this.