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Natural water bodies, such as lakes, rivers, and oceans, are important sources of atmospheric methane (CH₄). Therefore, quantitative and accurate determination of the dissolved CH₄ concentration in water is of great significance for studying CH₄ emissions and providing an in-depth understanding of the carbon cycle. Headspace gas chromatography (HGC) is the traditional method for measuring CH₄ in water. Despite its long success, it has a lot of problems in use, such as complex pretreatment and a long measurement time, and it is not suitable for the CH₄ determination of a large number of samples. In view of these shortcomings, a more convenient and efficient method based on membrane inlet mass spectrometry (MIMS) for quantitative measurements of the dissolved CH₄ concentration in water was established. In our study, the standard curves showed that the method had high accuracy, both at low and high CH₄ concentrations. After a laboratory test, to evaluate the sensitivity of this method, samples were collected from a large shallow lake (Lake Taihu). Both the HGC method and MIMS method were used to determine the dissolved CH₄ to compare these two methods. The small difference in CH₄ concentration obtained from the MIMS and HGC methods and the significant correlation between the CH₄ concentrations derived from the MIMS method with those derived from the HGC method showed that the MIMS method could replace the HGC method in the determination of dissolved CH₄ in natural waters. In addition, we also measured the sediment CH₄ production rates in three different areas of Lake Taihu using a laboratory incubation experiment. During the experiment, significant CH₄ accumulations were observed, indicating that sediment CH₄ production was an important source of dissolved CH₄ in the water column. Our study concluded that the MIMS method was sufficient and a better alternative than the HGC method owing to its capacity to measure a broad range of values plus the fact that it was relatively easy to use with less manipulation of the samples.