It's really impossible to say. "Lowlands Away" exists in many versions and certainly goes back to the nineteenth century. Some versions are about a dead lover; others are about poor pay and conditions for negro sailors, with the refrain "A dollar and a half a day". The reference to the Lowlands is probably a lyric fragment from an earlier ballad, possibly referring to the Netherlands, though it could be associated with the Lowlands of Virginia.

Here are some references:

From A. L. Lloyd's sleeve notes to Anne Briggs's version (1964):
"The song is a bit of a mystery. It has often been found in tradition in Britain and USA but always as a sailor shanty, usually sung while working at the pumps. Two distinct sets of words accompany the tune: one text tells the present story of the dead lover who returns; the other text concerns the work and pay of cotton-lumbers in the port of Mobile, Alabama. Deceived by the latter version, some specialists declare it to be a Negro song. More likely, it's a fragment of an Anglo-Scots ballad, full form forgotten, that lived on among British seamen who passed it on to longshoremen in the Gulf ports. The “Lowlands” refrain may be an echo from the old ballad of The Golden Vanity. Captain Whall, best of the pioneer shanty collectors, says that in Liverpool in the old days a crew of merchant seaman was often spoken of as “the Johns” so the term “my John” in the ballad is no more personal than “my lad”."
http://mainlynorfolk.info/anne.briggs/songs/lowlands.html

The Golden Vanity is about Sir Walter Raleigh building a ship in the Netherlands:
http://mainlynorfolk.info/lloyd/songs/thegoldenvanity.html

W. L. Alden commented in 1882:
"Perhaps the wildest, most mournful, of all sailor songs is "Lowlands." The chorus is even more than usually meaningless, but the song is the sighing of the wind and the throbbing of the restless ocean translated into melody."

The possible association with the Netherlands:

"This tune pattern ("Lowlands, lowlands away, my John...," with final line either "My lowlands away" or "My dollar and a half a day") has been used for at least three separate plots (which have perhaps cross-fertilized a bit): A dead sailor, a dead sailor's girl, and a more lyric piece about the bad conditions sailors face, the latter often having the "dollar and a half" refrain.
Shay, who apparently regards the dead sailor version as original, thinks this lyric item a much-decayed version of "The Lowlands of Holland." This is certainly possible, especially thematically, but there is a lot of evolution along the way...."

The foregoing is from the following thread, which contains a huge amount of information about this song and its possible origins and connections:
http://mudcat.org/thread.cfm?threadid=134132

"No versions collected from tradition have the "dream" lover: they are all complaints about the pay rates for cotton hoosiers in Mobile, or other Gulf ports, with the second refrain being not "Lowlands away", but "My dollar-and-a-half a day".
"Lowlands" is found in the chorus of several other shanties and sea songs, but the dream lover appears only in the forebitters:
- The Island Lass is given as a West Indian halyard shanty by Hugill, with a chorus of "Lowlands, lowlands, lowlands low"
- The Five Gallon Jar was sung at capstan and pumps, with a chorus of "In the old Virginia lowlands low".
- The Golden Vanity is not normally regarded as a shanty, but Hugill claims to have sung it at capstan and pumps, with its "Sailing in the lowlands low" chorus.
- Young Edwin in the Lowlands is not a shanty, but has the dead sailor appearing to his love in a dream
- The Lowlands of Holland has the apparition at the bedside, and the girl deciding to remove any trace of beauty or attractiveness, and may be where Masefield got the idea from."
http://www.shanty.org.uk/archive_songs/lowlands-away.html

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Note added at 8 hrs (2014-03-27 07:02:35 GMT)
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Could "my love is drowned in the windy Lowlands" ultimately echo a folk memory of the Anglo-Spanish conflict during the Dutch War of Independence (late sixteenth-early seventeenth century)? It seems a long shot, but who knows?