In his poem "To Marguerite--Continued," Matthew Arnold uses a question and answer device to conclude the poem, in which he poses a question and then answers it for the reader.  Your quote comprises the last three lines of the poem and make up the answer to Arnold's question which he asks at the beginning of the stanza.  In order to comprehend fully the last three lines of the poem, the reader must first examine the question that Arnold poses:

Who order'd, that their longing's fire
Should be, as soon as kindled, cool'd?
Who renders vain their deep desire?—

Arnold's query demands to know who is responsible for the separation of lovers, cooling their passion.  The speaker of the poem strongly answers this question in the last lines of the poem:

A God, a God their severance rul’d!
And bade betwixt their shores to be
The unplumb’d, salt, estranging sea.

According to the speaker of "To Marguerite--Continued," God is responsible for "their severance;" this line's use of the verb "rul'd" in conjunction with the exclamation mark at the end of the line forcefully declares God's role in separating the lovers.  The final two lines reinforce the extended metaphor posed earlier in the poem, depicting the "unplumb'd, slat, estranging sea" as a barrier dividing the lovers.  Arnold's diction, particularly 'unplumb'd' emphasizes the depth of their separation; 'plumb' is a verb used to show measurement. As Arnold shows the sea as "unplumb'd" he portrays the gulf between the lovers as being limitless and unfathomable.