To be honest I feel that I am unqualified to write anything coherent about this film .
The director, Shane Carruth, was responsible for Primer - an excellent film that I still haven't figured out the plot to yet (this diagram doesn't help much). Upstream Color is not quite so opaque (there is no time travel) but this is not a film you can watch halfheartedly.
Carruth's style of film making is best described as impressionistic. Stuff happens, but not everything relevant is shown. Time jumps, scenes start without announcing themselves, piling up into each other like chords in a symphony. Important dialog is omitted and it is up to the audience to piece together the fragments into as much coherence as they can muster. This is not to say that Upstream Color is an amateurish mess, like Primer it is a finely observed work where much is inferred but not stated and sometimes you have to mentally take a step back to take in the whole picture.
I thought the film's one major flaw was that the audience knew that both lead characters had been through the same experience long before the characters figured it out themselves. But this was probably a deliberate choice, the film concentrates on the characters' buttoned down emotional states rather than resolving the plot, although that does eventually happen as well.
Part horror, part love story, part study of mental illness, part picture of obsession, part indictment on amateur pig farming, Upstream Color is a hard film to explain. Would I recommended it? I enjoyed it, you might too.
Update: This article in the New Yorker gives as convincing explanation of what-the-hell-happened as any.