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Squirrels hate not having access to secure shelter or food sources. Your best line of defense is to make your property less attractive by removing access to these things. There are chemical squirrel repellents, but these have mixed success. According to Pennsylvania State University, you can apply products containing the bittering agent denatonium saccharide to a squirrel's favorite fence, tree, or roof spots. However, you need to reapply repellents regularly, which aren’t scientifically proven effective.

Squirrels are pretty skittish creatures, and they dread the presence of rodent-chasing dogs and cats. Sudden noises and bursts of activity can send them scampering away. Anything with an element of surprise, like motion-detecting lighting, strobe lights, and noisy wind chimes, can unsettle them. Even loud radios and voices can be perceived as threatening and terrifying to these furry critters.

Fleas are master hiders, so they’re always looking for safe spots. In addition to living directly on your pets, they’re likely to hide in bedding materials, not unlike the infamous bed bugs. They also like carpet and thick grass, for similar reasons. They’re more likely to hang around dirt and debris in general, which is why it’s important to keep the home clean. 

Identifying the specific animal running on your roof at night can be challenging without direct observation. Common nocturnal roof visitors include raccoons, squirrels, opossums, and rats. Raccoons are bigger and can create heavy thumping sounds. Squirrels are agile and may produce rapid scurrying noises. Opossums tend to move stealthily with less noise. Rats can make scratching or gnawing sounds. To determine the culprit, look for signs like footprints, droppings, or damaged areas near the roof. For accurate identification, consult a pest control professional or set up wildlife cameras near potential entry points.