Lost Answer - Why the Temple Pool Water was Murky
The question is: Why was the Temple pool water murky before Sayid was held under it? Dogen and his interpreter both seemed surprised that the water was not clear.
- The water had switched from being a vehicle for Jacob to being a vehicle for Man in Locke. The source of the water in the Temple pool is the water around the light in the cave, but the further it gets from the cave, the more easily it becomes tainted. After Jacob's death, Man in Locke was able to use the Temple water because the Temple was no longer protected by Jacob.
- The water comes from the same source or flows from the light cave. After the Swan Station imploded, the hydrodynamics of the water changed. Jacob was keeping things going, until he died. When Sayid was put into the pool, it had less healing ability. His body was healed, but he felt dead inside, with only a small glimmer of light, which Desmond was able to pull out, causing Sayid to redeem himself and act heroically in the end. Perhaps Rousseau's science team also stepped in the water when they went below the Temple and that is what changed them.
Source...