In this work, novel nonanol-based deep eutectic solvents (DESs) were synthesized from the various ammonium salts as hydrogen bond acceptors (HBAs) in a combination with 1-nonanol as a hydrogen bond donor (HBD). The synthesized hydrophobic DESs were characterized by measuring their physical properties including density, sound velocity, viscosity, electrical conductivity, surface tension, and refractive index as a function of temperature. Furthermore, a new method based on the prepared DESs was introduced for removal of Congo red, KMnO4, and K2Cr2O7from aqueous solutions with 100% efficiency, during 45–60 min of removal processes. Furthermore, one of the synthesized DESs was applied as qualitative and quantitative indicator for alanine, leucine, serine, glutamine, methionine, and glycine amino acids by spectrophotometry method.