The optimal conditions for pre-concentration of 90Sr from natural water samples by a T-3K carbonate-containing zirconium dioxide were determined. A method for determination of 90Sr in natural water samples was developed using the T-3K sorbent; the method provides as low detection limits as 0.03 Bq/L for 1L water samples and 0.02 Bq/L for 2L water samples. The method was tested on monitoring of 90Sr in natural water bodies at Sverdlovsk and Chelyabinsk regions as well as in waters of control and observation wells on the territory of a radioactive waste long-term storage facility. It was shown that the developed method can be used without control of strontium chemical yield in case of natural water samples containing up to 76 mg/L of Ca and 5.2 mmol/L of hardness salts taking into account the average strontium chemical yields of 91 ± 1% for 1L water samples and 81 ± 2%, for 2L water samples. In case of water samples with a higher hardness, the dependences of strontium yield on Ca concentration or hardness presented in this paper may be used for evaluation of strontium yield.