Ways of Protecting a Pool Heater
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Enclosure
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You can build a small enclosure with a waterproof roof and access door for your water-heater pump. Since the pump is not much larger than a large ice chest, the enclosure can be about the size of a medium doghouse. Set off from the pool deck, this small box can be as unobtrusive or ornate as you want. Just make sure the enclosure is large enough for good ventilation around the heater. Include some vents so air can easily pass through. When the pool is not in use during the winter months, these vents should be covered to protect the pump from extreme weather.
Underground
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An underground enclosure for your swimming-pool heater is really just a small hole in the ground with a concrete floor and cinder-block walls. With a flat or canted lid and ducted vents allowing air in and out (but no leaves, yard debris or small crawly things), this is a good option if your pool is installed in a dry climate. Free from ground water and moisture, the pump can operate freely, completely protected from the elements and out of eyesight.
House
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If you live in a slab house (with a solid concrete foundation), this option will probably not work. But if your house has a crawl space large enough for the swimming-pool heater pump, consider this space for an enclosure. House power can be brought to the heater pump and water-circulation lines can be brought either under the walls or through the ventilation vents around the raised foundation. Consider the slope under the house and whether or not there will need to be a drain installed. If the pump fails or there is a high-pressure water leak, the water has to drain. As long as this contingency is considered (which will only be a problem if the pump fails), then there's lots of covered protected space for your swimming-pool water heater right under your house.
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