It is important to eat appropriately to support high activity levels. On this basis, you should definitely track this, to ensure that your intake is sufficient.
However, there are good reasons to be conservative in your calorie estimates of treading water:
* your body gets efficient (ie. burns fewer calories) at anything it does regularly, and you are likely burning less calories than a non-regular swimmer who trod water for 2 hours
* the tracker assumes continuous activity, but I assume that at least some of this time you are holding on to the edge, or standing in shallow water.
So while you are in the water for 2 hours, perhaps tracking 60 minutes of treading water would be appropriate.