I am guessing that this isn't like the "rocket stoves" I have seen in the past, burning wood. If it is, you will have to ask yourself, what is the water being used for? If it's potable, I would not recommend venting the exhaust THROUGH the water, for contamination issues. If it's being recirculated, I would guess you will eventually have buildup of junk in your pipes and pump causing issues.
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