The thermal energy of a substance is the total amount of energy- potential and kinetic energy contained in it. It depends on the temperature, mass and phase of the substance.
Since, the both the containers contain liquid water at same temperature, greater mass would have greater thermal energy. Thus, container having 1000 mL of water would have greater thermal energy.
The easiest way to get a fairly accurate measure of your water flow rate is to time yourself filling up a bucket. So for example if you fill up a 10 litre bucket in 1.5 minutes, then your flow rate will be: 10/1.5 = 6.66 Litres per minute.
