Gaps in wood floors can usually be prevented by letting wood acclimate before installation. Wood filler won't help much, and will often make the floors look worse.
By the DIY experts of The Family Handyman Magazine
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Shrinkage cracks—and why filler won’t help
Plank flooring expands and contracts with humidity changes and may show some gaps. In fact, on old plank floors, gaps are considered part of the “look.” To minimize them, try keeping your home’s relative humidity close to 50 percent. During dry seasons or heating periods, the humidity often drops and you’ll need to use humidifiers. During periods of high humidity, you may have to dehumidify (although air conditioning often takes care of it).
I don’t recommend that you use a filler; it may look worse than the shrinkage gaps. A non-hardening color putty will fill the cracks, but it will dry and pop out within a year and need redoing. A putty that sets hard can create larger gaps or even buckle the floorboards by not leaving any expansion space. Conversely, it will crack if the floor shrinks.
The real cure for cracks in a wood plank floor is to minimize them in the first place. Here are the two main ways excessive cracks develop.
Excessive moisture 1. The wood flooring has too much moisture content when installed and then shrinks as it “dries out.” The solution is to buy dry wood and to acclimate the flooring to the room you want to lay it in. All work that introduces moisture (concrete floors, drywall taping and texturing, painting) must be complete and dry. Then store the wood on location for at least two weeks. A normal humidity level must be maintained during this period (by heating or air conditioning).
Compression set 2. The wood is too dry to start with and the flooring absorbs excessive moisture after installation. As the wood expands, the pressure will crush fibers at the edge of the boards along tight joints. This is called compression set. When the wood dries out again, it will shrink; the crushed fibers won’t completely rebound and a gap will form. Again, the solution is to acclimate the wood to the space, making sure the humidity is kept close to its normal level.
In all cases, put a coat of finish on new floors as soon as possible, as this will slow down moisture movement into and out of the wood floor planks.