The first mineralogical and geochemical investigation of the travertine limestone, soil and corresponding plants associated with the Neogene basin of Varnavas, NE Attica, revealed a significant enrichment in the metalloid As. The total concentrations of As ranged from 61 to 210 ppm in limestone and 33 to 430 ppm in the associated soil demonstrating a wide variation of values. Calcite is a common authigenic mineral within travertine limestone, forming fine uniform micritic aggregates, having As and Mg concentrations lower than detection limits of EDS analysis. Clastic dominated minerals are quartz (both fine- and coarse-grained), muscovite, clinochlore, illite, pyrite, galena, arsenides, rutile, sphene, zircon, REE-minerals and albite. Goethite and Fe-Mn-oxides occur between calcite grains. The presence of fossilized micro organisms, resembling foraminifera, in travertine limestone combined with hydrous Fe-Mn-oxides, suggests a possible marine transgression during the evolution of the basin. The As content in plants ranges from 1.1 to 28 ppm As in shoots, and 0.8 to 114 ppm As in roots. The translocation factor, which is defined as the ratio of metal concentration in the shoots to the roots, is relatively low (average 0.33%) suggesting that the internal transport of metals from the roots to shoots was restricted. The bioaccumulation factor, which is defined as the ratio of metal concentration in the plants to that in soil, exhibits a wide range from relatively low (5.2–9.0% for As, Fe, Cr, Ni and Pb), much higher (56–67% for Cu and Zn) and exceptionally high (160% for Mo). A significant correlation between the translocation factors for Fe and As may confirm that Fe-Mn oxides/hydroxides represent the major sorbing agents for As in soils. The presented data, due to As contamination in travertine limestone, soil and plants, suggest a potential environmental risk not only for that part of Greece but in general for similar depositional environments.