The water in temple spring is brown, Sayid dies after dunking

Dogen leads the surviors through the temple where we can see a few natives/others working the the grounds. They are then led to the interior where the spring is located. Hieroglyphics are visible on the pillars of the room.

As they enter, Lennon notes that the water isn't clear and asks what happened. Dogen says that he doesn't know and proceeds to the steps of the spring, cuts his hand with a knife and submerges it in the water for a few seconds. He pulls it out and it hasn't healed. He then tells them that there will be risks if they heal Sayid and Jack, continuing his new trust fate kick, immediately agrees that they should proceed.

A few of the men remove Sayid's coveralls and proceed to carry him into the spring. They submerge him once Dogen has started an hourglass which appears to be filled with a mix of dark and light sand. Sayid starts kicking fairly quickly but they keep him down until the hourglass runs out and he is no longer moving. Sayid is in a Christ-like pose as he is carried from the spring and then Dogen confirms that he is dead.

Jack then briefly tries to resuscitate Sayid (which is similar to when he saved Charlie after he was hung  by Ethan), but gives up at Kate's insistence.

So was the water not clear because Jacob is dead? What exactly is the spring and how does it work? Presumably, this is where Richard brought Ben after Sayid shot him.