"The Pocket Bible Dictionary": Philip Schaff; Jubilee Publishers edition, p. 125-126 reminds us that "Jordan" means "the Descender" and that 'the Jordan river, the principal river of Palestine, has four sources, which are situated among the mountains.."
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Would being situated in the mountains account for the Jordan River's waters being "chilly and cold?"
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"The Pocket Bible Dictionary" also has the following passage:
"The Jordan is first mentioned in Genesis 13:10; it was crossed by Jacob, Gen.32:29 and passed over by the Isrealites when entering the Promised Land., Josh 3:14, Ps.114:3. It is mentioned many times in the Old Testement, and wonderful miracles are connected with it, among which is the curing of Naaman 2 Kings 5:14. The principal events associated with it in the New Testament are the baptism of the multitudes by John the Baptist, Matt. 3:6 and [the baptism]of Jesus Mark 1:9.
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The idea of "cross roads" is an extremely important African concept. The River Jordan was THE symbol for enslaved Africans of the dividing line between life & death; earth & heaven.

I believe that rivers and the Jordan River might have also been used as a symbol for the other important division in enslaved African Americans'lives: slavery and freedom.

Although not directly related to the song 'Yonder Come Day', if rivers are used in religious and secular African American slave songs to denote the means by which people could achieve freedom from slavery, we may need to re-think all the possible meanings of the widely used floating verse "I went to the river, but I couldn't get across..."