Yes, this is basically the correct approach. Strictly speaking, some of the energy you put in will go into heating the water, i.e., the water will get hotter as you agitate it. The energy balance would be something like:

$$ \Delta E = W + C\Delta T $$

where $C$ is the specific heat and $\Delta T$ the temperature rise. However, under most conditions, the temperature rise will be small enough that it can be ignored.