Previous studies have demonstrated both mass-dependent fractionation (MDF) and mass-independent fractionation (MIF) of Hg isotopes in the environment and the potential for their application in biochemistry and geochemistry. However, little has been reported for Hg isotope geochemistry in natural aqueous environment due to the very low concentration (1–20 ng/L). We report here, for the first time, a new protocol for directly pre-concentrating Hg using AG 1 × 4 ion-exchange resin, which allows the measurement of Hg isotope composition in freshwater samples. The protocol is validated by testing both synthetic and natural solutions of varying concentrations, and by assessing the effect of Hg recovery and organic complexants on the reproducibility and the accuracy of measured isotopic ratios. The method results in acceptable procedural blanks and quantitative yields (101% ± 6%) in the final Hg eluates. The instrumental mass bias was corrected using modified empirical external normalization (MEEN) with Tl as internal dopant. The sensitivity of the method to the solution matrix (Hg/Tl ratio, organic matter concentration) was also evaluated. The pre-concentration and isotopic measurement protocol was applied to 16 natural water samples with Hg concentrations ranging from 0.9 ng/L to 15600 ng/L. The result showed a total variation of 2.4‰ for δ202Hg and evident MDF and MIF of Hg isotopes. Our study demonstrates that more research is required to fully understand the behavior of Hg isotopes in the aqueous environment.