Thermal efficiency would be almost impossible to measure on a water heater. But on boilers and furnaces it is easy to measure, in fact it is the only efficiency that is possible to accurately measure.
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To get an accurate thermal efficiency on a boiler you need to have know the GPM through the boiler. Then measure delta T. BTUH = GPM x Delta T x 500. Then clock the meter.
If you clock the meter at 100,000 BTUH and measure 75,000 BTUH leaving the boiler, you know that your thermal efficiency is 75%.
On a furnace you need to measure CFM and temp rise. CFM x Temp rise x 1.08 will give you the output.
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