A key challenge in climate change research is apportioning the greenhouse gas methane (CH4) between various natural and anthropogenic sources. Isotopic source fingerprinting of CH4 releases, particularly with radiocarbon analysis, is a promising approach. Here, we establish an analytical protocol for preparing CH4 from seawater and other aqueous matrices for high-precision natural abundance radiocarbon measurement. Methane is stripped from water in the optionally field-operated system (STRIPS), followed by shore-based purification and conversion to carbon dioxide (CO2) in the CH4 Isotope Preparation System (CHIPS) to allow Accelerator Mass Spectrometry analysis. The blank (±1σ) of the combined STRIPS and CHIPS is low (0.67 ± 0.12 μg C), allowing natural sample sizes down to 10 μg C-CH4 (i.e., 30 L samples of 40 nM CH4). The full-system yield is >90% for both CH4-spiked seawater and ambient samples from CH4 hotspots in the Baltic Sea and the Arctic Ocean. Furthermore, the radiocarbon isotope signal of CH4 remains constant through the multistage processing in the STRIPS and the CHIPS. The developed method thus allows for in-field sampling and sample size reduction followed by precise and CH4-specific radiocarbon analysis. This enables powerful source apportionment of CH4 emitted from aquatic systems from the tropics to the polar regions.