The ion content of drinking water might be associated with urinary stone formation, representing a keystone of conservative nephrolithiasis management. However, the effects of specific ions on calcium oxalate crystal formation and their mechanism of action are still highly controversial. We report an investigation of the effects of oligomineral waters with similar total salt amount but different ion composition on calcium oxalate (CaOx) precipitation in vitro, combining gravimetric and microscopic assays. The results suggest that the “collective” physicochemical properties of the aqueous medium, deriving from the ion combination rather than from a single ionic species, are of importance. Particularly, the ability of ions to strengthen/weaken the aqueous medium structure determines an increase/decrease in the interfacial energy, modulating the formation and growth of CaOx crystals.