The natural zeolite from Evros prefecture contains Ca-rich clinoptilolite (89 wt.%) and in total 92 wt.% microporous minerals (zeolite + mica + clays). Quartz and feldspars constitute the non-microporous minerals (8 wt.%). Acidic water (pH 5.5) from the Kokkinolakkas Stream and basic water (pH 9.5) from the Koronia Lake were treated with the Evros natural zeolite. An intense increase in the pH was recorded in the acidic Stream water, while a pH decrease occurred in the basic lake water. These observations demonstrate that the zeolite tends to neutralize the water acting either as a proton acceptor or as a proton donor, exhibiting thus an amphoteric character. It should also be emphasized that near the neutral pH range, a faster increase of the pH towards the basic area was initially observed, followed by a slower decrease until its stabilization. In addition, a remarkable improvement of the clearness of both waters was observed.