In the present paper the fractional calculus is involved as an effective tool, aiming to study the water percolation into the porous soil. This is a more accurate treatment of the diffusion in the aquifers. The described phenomenon is seen as a natural water filtration system whose features are better depicted by the fractional derivative, occurring into the Fick law of diffusion. The actual analysis is one dimensional, making the task as easy as possible in order to emphasize the great utility of the fractional frame of work. In the final section, the paper is trying to reach the highly important problem of the groundwater contamination.