As one of the most concerned radionuclides, 99technetium (Tc) usually exists as pertechnetate (TcO4−) and low-valence Tc(IV) in the environment. The speciation analysis of 99Tc plays a crucial role in understanding its toxicity, bioavailability and mobility, and developing effective remediation strategies. However, conventional hyphenated techniques for 99Tc speciation analysis usually require a large sample volume and tedious operation process. In this work, a simple but highly effective system, coupling capillary electrophoresis to inductively coupled plasma mass spectrometry (CE-ICP-MS), was developed to analyze total rhenium (TRe), Re(IV), and Re(VII), known as the analogues of technetium. It is worth noting that by the use of a sprayer with a direct-injection nebulizer as the interface, the CE and ICP-MS were efficiently coupled as an entity that shares the advantages of both modules. In comparison to conventional techniques, the proposed CE-ICP-MS dominates in terms of less sample consumption and higher sample introduction efficiency, thus results in improved sensitivity, reduced radioactive waste, and more significantly, alleviated radiological exposure to operators. Under the optimized conditions, LODs of 0.02 μg L−1 and 0.01 μg L−1 were obtained for TRe and Re(VII), respectively, with relative standard deviations (RSDs) better than 3.0%. In addition, the accuracy and practicability of this hyphenated system were validated by analyzing simulated Hanford site groundwater samples with satisfactory recovery and separation of TRe, Re(IV), and Re(VII). The proposed method retains the great potential for the speciation analysis of 99Tc in various samples.