Wired magazine has a profile on The Fountain and Darren Aronofsky's six year journey to make it. To keep the budget down and cultivate a novel sci-fi look, they hired a team which uses microscopic video of particles in liquid to create the special effects:

Bristling with digital and film cameras, lenses, and Victorian prisms, their contraption can magnify a microliter of water up to 500,000 times or fill an Imax screen with the period at the end of this sentence. Into water they sprinkle yeast, dyes, solvents, and baby oil, along with other ingredients they decline to divulge. The secret of Parks' technique is an odd law of fluid dynamics: The less fluid you have, the more it behaves like a solid. The upshot is that Parks can make a dash of curry powder cascading toward the lens look like an onslaught of flaming meteorites. "When these images are projected on a big screen, you feel like you're looking at infinity," he says. "That's because the same forces at work in the water – gravitational effects, settlement, refractive indices – are happening in outer space." The microzoom optical bench furnished Aronofsky's film with something neither a computer nor an old-fashioned matte painter could deliver – chaos, in all its ultra high-definition fractal glory.