There are a few different things that can cause brown stains on vinyl pool liners. The most common culprit is dirt and debris that has been allowed to build up on the liner. When this happens, it can create a perfect environment for algae to grow, which can also lead to brown stains. Other causes of brown stains on vinyl pool liners include leaves, twigs, and other organic matter that have fallen into the pool. Thankfully, removing these stains is usually easy and doesn't require any special cleaners or chemicals.