Hi Gbisson51,
For me to answer your question I’d have to know several conditions related to your water heater and chimney installation which you didn’t describe. Therefore I can only give a general list of things that might cause water seepage… they may not apply to your situation at all.
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deteriorated walls of a brick / stone / cinder block chimney, missing mortar
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corroded walls (with holes) of a metal chimney
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damaged / deteriorating / missing chimney cap
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high water table (assuming that your masonry chimney sits on the basement’s floor) that causes seepage from under the chimney
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deteriorated moisture membrane on a chimney section beneath the ground level (common issue on chimneys located on a side wall of the house / extending into the basement)
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leaking chimney flashing at roof penetration
You can call your local chimney sweep, a plumber, or an HVAC contractor to trace this problem, however, if it is related to your drainage system (water penetrating from under the basement’s floor or chimney’s underground section, drainage / waterproofing company might be required.
Just click “comment” below if you have more question, try to explain your installation (chimney type, location / positioning inside the house, cap, etc.) and describe where is the water coming from in as much detail as possible.