Just came across this problem with my 3.0 D4D, water in fuel light came on so turned the truck off and drained the fuel filter, pumped it back up and kept driving, the light now stayed on constant. So during the week I replaced the fuel filter, but the light still stayed on. Did a bit of research and found that you have to reset the ignition to clear light.
1. Pull electrical plug off the top of the filter.
2. Start car and re connect the plug
3. After 3 seconds the light will clear
PROBLEM SOLVED!!

Toddie