RE: Tracer Dyes. These are often designed so that even if the dye isn't visibile to the naked eye by exposing a sample of water to UV light the dye glows in a way that can be detected electronically.
In this way the dye can still be detected when it is diluted down to levels way below is being visible to the naked eye. In fact in some situations where they are used this is the preferred method. For example releasing the dye into a stream at the start of a cave network and sampling the rivers coming out of the caves to see if they are connected. The locals tend to get funny if you turn the whole rivers purple, hence using dyes at levels to be invisible to the naked eye, but still detectable is standard practise.
So in the AF scenario by taking samples of surface water and testing for presence of the dye over a very wide area you could find traces and focus the search in to the areas with the highest concentrations.