This particular song is said to come from slaves before the American Civil War. It was first recorded by the Fisk Jubilee Singers in 1915, with its most famous version being recorded by the Swan Silvertones. I don't like that version at all.
In the song, "Mary" might refer to the Virgin Mary but more likely the singer is talking about Miriam, the sister of Aaron and Moses, unless they're talking about Mary the sister of Lazarus, or...there's a few Marys.
Now as for the lyrics...the Fisk Island Jubilee singers are doing a different version than most people do. Here I try to transcribe the lyrics as best i can, for I can find no place where they're written out completely.
REFRAIN:
Oh, Mary, don't you weep don't you mourn,
Oh, Mary, don't you weep don't you mourn
Because Pharaoh's Army got Drownded,
Oh, Mary, Don't you weep --
Oh, Mary, don't you weep don't you mourn,
Oh, Mary, don't you weep don't you mourn
Because Pharaoh's Army got Drownded,
Oh, Mary, Don't you weep
I don't know what my mother wants to stay here for,
This old world ain't no friend to her
Because Pharaoh's Army got Drownded,
Oh, Mary, Don't you weep.
Refrain
Some of these mornings bright and fair
Gonna take my wings and cleave the air
Because Pharaoh's Army got Drownded,
Oh, Mary, Don't you weep.
Refrain
When I get to heaven going to put on my shoes
Gonna run around glory and tell all the news
Because Pharaoh's Army got Drownded,
Oh, Mary, Don't you weep.
Refrain
When I get to heaven going to sing and shout
Nobody there to turn me out
Because Pharaoh's Army got Drownded,
Oh, Mary, Don't you weep.
Refrain
Now that's the Fisk version; here's the version most other people use.
Refrain:
Oh, Mary, don't you weep don't you mourn,
Oh, Mary, don't you weep don't you mourn
Because Pharaoh's Army got Drownded,
Oh, Mary, Don't you weep --
If I could I surely would
Stand on the rock where Moses stood
Pharoah's army got drownded
Oh Mary don't you weep
Refrain
Mary wore three links of chain
Every link was Jesus' name
Pharoah's army got drownded
Oh Mary don't you weep
Refrain
One of these nights about 12 o' clock
This old worlds going to reel and rock
Pharoah's army got drownded
Oh Mary don't you weep
Refrain
God told Moses what to do
To lead the Hebrew children through
Pharoah's army got drownded
Oh Mary don't you weep
Refrain
Moses stood on the red sea shore
Smotin' the water with a two by four
Pharoah's army got drownded
Oh Mary don't you weep
Refrain
God gave Noah the rainbow sign
No more water, but fire next time
Pharoah's army got drownded
Oh Mary don't you weep
Refrain
Mary wore three links of chain
Every link was freedoms name
Pharoah's army got drownded
Oh Mary don't you weep
Refrain
The very moment I thought I was lost
The dungeon shook and the chains fell off
Pharoah's army got drownded
Oh Mary don't you weep
Refrain
I may be right and I may be wrong
I know you're gonna miss me when I am gone
Pharoah's army got drownded
Oh Mary don't you weep
Refrain