Walter Jones was born in Baltimore, Maryland. He was educated at Johns Hopkins University, where he received his B.A. in 1888 and his Ph.D. in 1891. He served as professor of chemistry at Wittenberg College for 1 year, and then from 1892 to 1895 he was professor of analytical chemistry at Purdue University in Indiana. He returned to Johns Hopkins in 1895 to work in the Physiological Chemistry Department, first as assistant and associate, then as associate professor, and finally as professor of physiological chemistry. He retired as professor emeritus in 1927.
Jones' work explored nucleic acids and their derivatives, chemical properties, and physiological conduct. The Journal of Biological Chemistry, especially from 1904–1917, published a long list of papers from Jones' laboratory. Particularly noteworthy was his research showing the action of enzymes in the breaking down of nucleic acids, the mode of nucleotide linkage in yeast nucleic acid, and the structure of the purine mononucleotides. Jones believed the experimental evidence indicated that the nucleotide groups of yeast nucleic acid are joined together through their carbohydrate groups, giving rise to a polysaccharide structure. Jones was president of the American Society of Biological Chemists for two terms, 1915 and 1916, and was elected to the National Academy of Sciences in 1918.