Sagittal otoliths are typically composed of the aragonitic calcium carbonate (CaCO3) polymorph, but the aragonitic sagitta are often laid down with vaterite, another CaCO3 polymorph. Several studies have suggested some factors which may be responsible for the vateritization, but the mechanisms remain unresolved. Here, we experimentally demonstrated that rearing in strontium (Sr)-added water induces vateritization of sagittal otolith in an inbred strain of Oryzias latipes. Fertilized eggs were randomly assigned to the Sr-rich group and the control group and were individually kept for 4 months. The crystal structure of each sagittal otolith was determined by Raman spectroscopic analysis. The Raman result indicated that vateritized otoliths occurred only in the Sr-rich group. Daily changes of Sr/Ca concentrations were evaluated using electron probe micro analyzer (EPMA). The EPMA result revealed that the Sr/Ca gradually increased throughout the aragonitic phase following the abrupt reduction at the transition to the vateritic phase. Our results support that experimental approach with chemically adjusted water helps to reveal the mechanisms for the vateritization as well as to investigate the effect of equipping vateritized otoliths on fishes.