If you have a lot of water in the tank the car won't run, as water is always heavier than the fuel and the pump always sucks directly from the bottom. You don't want to try to pump it dry with the pump. Best bet is to drive it until the problem reappears and check the output and pressure with the proper gauge. You may have a marginal pump. The pump depends on the fuel as its coolant and lubricant and large amounts of alcohol or whatever you're using as a dessicant are only going to make things worse.
Remember, pumps always push better than suck. (OW! I just bit my lip...
) As a pump worsens its ability to lift will deteriorate first. The weight of the full tank of fuel may be the reason for it not showing until almost drained.