Variation in strontium (Sr) and barium (Ba) within otoliths is invaluable to studies of fish diadromy. Typically, otolith Sr:Ca is positively related to salinity, and the ratios of Ba and Sr to calcium (Ca) vary in opposite directions in relation to salinity. In this study of jungle perch, Kuhlia rupestris, otolith Sr : Ca and Ba : Ca, however, showed the same rapid increase as late-larval stages transitioned directly from a marine to freshwater environment. This transition was indicated by a microstructural check mark on otoliths at 35-45 days age. As expected ambient Sr was lower in the fresh than the marine water, however, low Ca levels (0.4 mg L-1) of the freshwater resulted in the Sr:Ca being substantially higher than the marine water. Importantly, the otolith Sr:Ba ratio showed the expected pattern of a decrease from the marine to freshwater stage, illustrating that Sr:Ba provided a more reliable inference of diadromous behaviour based on prior expectations of their relationship to salinity, than did Sr:Ca. The results demonstrate that Ca variation in freshwaters can potentially be an important influence on otolith element:Ca ratios and that inferences of marine-freshwater habitat use from otolith Sr:Ca alone can be problematic without an understanding of water chemistry.