can salt water flowin in from the sea be filtered naturally by the soil, perhaps with specific desalinating minerals, into fresh water?
You are looking for a way to naturally desalinize water.
Sorry to disappoint you, but it requires energy to happen, thus I don't think it can happen by simple filtration.
Desalination is a process that takes away mineral components from saline water.
The closes you can get in a natural environment is one of the following:
First reverse osmosis
The leading process for desalination in terms of installed capacity and yearly growth is reverse osmosis (RO). The RO membrane processes use semipermeable membranes and applied pressure (on the membrane feed side) to preferentially induce water permeation through the membrane while rejecting salts. Reverse osmosis plant membrane systems typically use less energy than thermal desalination processes.
Or also freeze-taw
Freeze-thaw desalination uses freezing to remove fresh water from salt water. Salt water is sprayed during freezing conditions into a pad where an ice-pile builds up. When seasonal conditions warm, naturally desalinated melt water is recovered. This technique relies on extended periods of natural sub-freezing conditions.
Or, finally, solar evaporation
Solar evaporation mimics the natural water cycle, in which the sun heats the sea water enough for evaporation to occur. After evaporation, the water vapor is condensed onto a cool surface.