Microbial methane oxidation rates in ocean and freshwater systems reveal how much of emitted methane from the sediments is oxidized to CO2 and how much can reach the atmosphere directly. The tracer-method using 3H-CH4 provides a way to measure methane oxidation rates even in water with low methane concentrations. We assessed this method by implementing several experiments, collecting data from various environments, and including recent literature concerning the method to identify any uncertainties that should be considered. Our assessment reveals some difficulties of the method but also reassures previous assumptions to be correct. Some of the difficulties are hardly to be avoided, such as incubating all samples at the right in situ temperature or limiting the variability of methane oxidation rate measurements in water of low methanotrophic activity. Other details, for example, quickly measuring the total radioactivity after stopping the incubation, are easy to adapt in each laboratory. And yet other details as shaking during incubation and bottle size seem to be irrelevant. With our study, we hope to improve and to encourage future measurements of methane oxidation rates in different environments and to provide a standard procedure of methane oxidation rate measurements to make the data better comparable.