About 2 years ago we had a problem with what appeared to be 'emulsified' fuel in the aft tank. The stuff looked like strawberry milk. We spoke with a fuel polishing expert (ha, ha!) at the Va Beach boat show and he stated that the problem was water in the fuel. A friend of mine runs an environmental lab and we gave him a sample to analyze. Turns out that there was no detectable water in the fuel, fresh or saltwater. I had the aft tank emptied and cleaned and we put another 50 gallons of clean diesel in the tank. Ran the boat for five minutes and had the same problem. I eventually figured out that it was an air leak in the fuel return line (i.e. there was no fuel leaking on the suction side). I replaced the old copper tubing with fuel hose and the problem disappeared immediately.
Obviously, the point is that you may not want to assume that water in your fuel that is causing the problem.