If your winter boots are lined with a waterproof material, check to make sure they're waterproof on the surface, too. Weblog Refinery29 notes that even if the liner is waterproof, water can become trapped between the liner and the outer material. This can cause water spots to mark your boots.
Image from stevendepolo
You can quickly check your boots by wetting them and making sure the droplets slide right off. If they aren't, you can easily waterproof them with beeswax or Rust-oleum, depending on the material. For more tips on winterising your boots, check out the full post linked below.