If I am lowered and took out the fender lining of my car is there a chance water can get into the headlight. Because there's water in it right now. But I don't know if it's from the rain, or the humidity in my garage.

 

either the headlight has been opened before and sealed badly or theres a hole somewhere in the headlight, could be a crack in the back, or a bad bulb gasket

 

Probably just condensation. Remove headlights, let them dry out completely, and reseal them.

Why did you remove your fender liners? All you would have to do is trim them were the tires were rubbing, or let the tires were the plastic lining out on its own. I was lowered around 2.75" with 19x9.5 +22 wheels and I just trimmed my liner slightly and never had any problems.