First of all, what kind of Boat, and how long have you owned it?
Boats do sit the water, so there are lots of places for water get in. Outboard, Inboard, Stern Drive, or Jet Drive all have leakage points unique to them
Do you use it for water sports? What colour is the bilge. and how good is the lighting when you are checking?
Any hole, or fitting that goes thru the Hull is a potential leak, so is the seam where the hull, deck and cap are joined.
Any impact damage to the hull? Any repaired areas? Are there any cracks in the hull? Missing Fittings?
Do you have any live wells? Any under seat/cushion Cold Drink storage, where you put ice?
Painting the hull won't seal it, and will hide evidence of Damage.
Water is getting in. You are going to have to do some Detective work.
Someone will suggest filling the boat with water when on a trailer, with the reasoning that 'where the water got it in. it will drain out'. That might work, but it can overload a trailer very quickly in addition to putting stress on hull as the trailer supports aren't large/numerous enough for the extra weight.