Organic dyes and toxic heavy metals are among the most serious environmental pollutants and pose a great concern to human health since they are not biodegradable. This paper reports the application of modified natural clay minerals in removal of toxic chromium (VI) ion and methyl-red dye from aqueous solution. Three different types of clay minerals namely Zemero, Seladengay and Mehal Meda clays were collected from different parts of North Shoa Zone, Amhara region, Ethiopia, and then their surfaces were separately modified with different amount of hydrochloric acid (15%, 20%, and 25%), nitric acid (15%, 20%, and 25%) and sulfuric acid (15%, 20%, and 25%). The concentration of chromium (VI) was determined using Atomic Absorption Spectroscopy before and after treatment with the activated clay minerals. UV-Visible Spectrophotometer was used to determine concentration of dyes before and after treatment of the methyl red solution with modified clays. The results demonstrated that Zemero clay mineral modified with 25% of H2SO4 was more efficient in removing methyl-red from aqueous solution compared to Seladengay and Mehal Meda clay minerals activated with the same acid under similar conditions. Chromium (VI) ion (96.99%) and methyl-red (99.33%) from aqueous solution were removed by sulfuric acid modified Zemero clay, indicating the potential of the clay minerals for removal of toxic chemicals from water.