I've noticed this problem in a lot of maps -- people use non-transparent water for a sludgy effect, but the water, being non-transparent, also blocks vis and light. This means the area under the water is black, so when players are in the water and get their lighting information from the ground there, they're also black. Also, it can lead to built-in "wallhacks" where people can move to the edge of the water and see entities but not walls (popular on the fort20 waterfalls). The solution is simple. Apply the translucent flag in the surface properties. This allows light and vis to pass through. I'll post some screenshots and a sample map later.
