It's a metaphor for building peace in a region both "sacred and profane" by "making sacred" its "profanity," i.e., purifying the river.
The purified river, by collecting in its arid watershed the sacred and profane, would help build peace between the Middle East’s two archenemies.
"Blessed. Cursed. Claimed. On foot through the Holy Lands," Paul Salopek. National Geographic Magazine. December 2014.
Israel and Palestine are "the Middle East's two archenemies" in this context.
The land and the history of that land as "the birthplace of supreme deities" (ibid.), is "the sacred."
The river undergoing purification, "a river of raw sewage that foams in torrents" (ibid.), is "the profane."
And the project to "clean up the waste...and establish miles of “green” trails" (ibid.) is "the purified river."
Also, the Fertile Crescent, as a part of the Middle East, is the "arid watershed."
And the arid watershed, by its mere location, has to "collect" whatever humans leave in it, including "the sacred and profane."
What gives this sentence its depth (and beauty, if I may say so), however, is the literal meaning of the words sacred and profane used within this figurative context.
The profane is that which "violate[s] the sacred or the good," ("Profane," Wikipedia).
Thus, to be sacred, one must remove the profane, through purification ("Ritual purification," Wikipedia).
Thus, in an essay about one man's endeavor "to clean up the waste...and establish miles of “green” trails along a fabled valley where 5,000 years ago[,] ['a holy city in the three major Abrahamic religions of Judaism, Christianity and Islam' (1)] was founded" (2), it's quite apt to see the appearance of the words the sacred and the profane.
(1) "Jerusalem," Wikipedia.
(2) "Blessed. Cursed. Claimed."
Even Longer Answer
And then, of course, there is the reason that this sentence is truly profound, and that is, of course, as a metaphor for the tumultuous region known as the Middle East.
The project to "clean up the waste...and establish miles of 'green' trails" ("Blessed. Cursed. Claimed.") is used by the author as a metaphor for peace.
And because the waste, the effluent, ironically, can cross borders where people cannot ("Israeli West Bank barrier, Reduced Freedoms," Wikipedia), the project hopes to "bridge the lives of Palestinians and Israelis" (ibid.) physically where politics cannot.
Quite a beautiful piece of writing. Thanks for sharing!