The fuel companies check their tanks (Storage and Tanker) for the presence of water etc.
Water detection paste or other similar methods are used to test fuel samples for water.
If clear of water and other contaminants, the fuel is supplied to the aircraft.
As you alluded to, water is usually suspended in the Avtur and draining from the lowest point in a fuel tank is not a definitive check for the presence of water. That is why it has to be tested before it is put into the aircraft.
The PIC is indemnified by the fuel record carried onboard the aircraft, that the fuel has been tested for and found free of contaminents by the fuel suppliers.
When all of these procedures have been verified by the PIC or delegate, they 'sign' for the fuel (Type, Quantity, Quality, SG and Loading).
Hope this helps.