Water in your gas would make it stall. How it gets in there is from condensation.
Gas has up to 10% Ethenol in it. Ethenol attracts water. When your tank sits part way to all the way empty, the empty void gets condensation and that is the primary way your water in the gas comes from.
You should be using some type of fuel stabilizer like Sta-bil, Startron, or SeaFoam in your gas to combat this.
Mechanics can check to see if there is water in your gas. The good news is, this is an easy fix!
Put only enough gas in your tanks that you will use each time out plus alittle extra for a reserve and put the fuel stabilizer in it, or fill your tank and top it off each time you are done on the water and also include the fuel stabilizer of your choice.
But YES, water in your fuel will cause your engine to stall.
I hope this helps!