Most fuel filters are designed to filter out solid matter to a certain micron rating. Water (for example) is not a solid and will pass straight through such a filter.

Even if you have an aftermarket fuel filter and water separator with a sight glass (which would show you water passing through to your engine either separated as droplets or in a milky-looking fuel-water emulsion), they are only able to remove the water droplets. Once fuel emulsifies with water, filters and separators cannot distinguish between the two.