Is this on top of the tank or what is in the fuel filter bowl? Water and crud in the tank is on the bottom and comes out first. Whats on top is fuel. Tanks are difficult to clean in place. I would get setup and work the filters hard.
Here is a previous post I did on the subject...
If it ran for 20 minuets then died you immediately need to pull the filter can off and dump into a somewhat clear plastic quart container (West, Home Depot or takeout). Or a glass jar as seasick said. It will take less than a minute for the fuel to separate from the water.
It's difficult to get all the water out of the tanks at the dock. I found that running the boat and bouncing around gets the water somewhat in suspension where the pickup in the tank gets fuel and a little water up into the filter. Remember the water sits on the bottom of the tank and the fuel floats. And it takes a while to fill the fuel filter up with water - maybe 20 minuets in your case.
Once it stalls you need to get the water out of both the can filter and the one on the engine. I bring a small can of gas with me and a disposal container (orange juice bottle). Dump the filter can into a container, give it a minute, dump only the fuel back in the filter, top off a little with fresh fuel and put it back up. Same with the filter on the engine. Pull cowling off, unscrew filter, dump into container, give it a minute, dump only the fuel back in the filter, top off a little with fresh fuel and put it back up.
I don't really like messing with fuel out on the water but its the only way it works for me. Always have someone with you and a good fire extinguisher handy.
The alternative is to run the boat for a while, shut the motor down, inspect the bowl on the Sierra clear bowl. If you see water tap it off into a container. Start more back up and run around. Re-check again.
It's really important that you deal with the water in the larger filter can BEFORE it gets up into the engine. Otherwise you will stall the engine and have a hard time restarting it.