The upper Miocene of Karlovassi Basin, Samos Island, Greece, contain continental evaporites such as colemanite, ulexite, celestite, gypsum and thenardite. These evaporites are related with volcanic tuffs, diagenetically altered in a saline-alkaline lake environment. The aim of the present paper is to: a) define the impact of the already known and possible buried borates and other evaporites to the geochemistry of the hydrogeological system of Karlovassi Basin, and; b) to assess the correlation between surface and underground evaporite deposits considering the spatial changes in the concentrations of the examined physicochemical parameters. Fieldwork, laboratory measurements and literature data revealed elevated boron values (2136–33012 ⧎/L) in the central part of Karlovassi Basin. In the same area, high amounts of strontium, sodium, lithium and sulfates also occur. It is proposed that these ions originate from the leaching of evaporites and authigenic minerals such as the Sr-rich clinoptilolite and the boron-bearing potassium feldspar. Boron values are abnormally high for freshwater aquifers, and are indicative of the presence of buried evaporites in the basin with unknown significance.