Methane oxidation in lakes constrains the methane emissions to the atmosphere and simultaneously enables the transfer of methane carbon to pelagic food webs. Several different methods have been used to estimate methane oxidation, but these methods have not previously been compared. In this study, we present methane oxidation estimates from three different lakes during summer and winter, using methods based on the transformation of added 14CH4, the fractionation of natural methane 13C, and the mass balance modeling of concentration gradients. All methods yielded similar results, including similar differences between lakes and seasons. Average methane oxidation rates varied from 0.25 to 81 mg of C m(-2) d(-1) and indicatethatthethree methods are comparable, although they to some extent take different processes into account. Critical issues as well as drawbacks and advantages with the used methods are thoroughly discussed. We conclude that methods using the stable isotope or mass balance modeling approach represent promising alternatives, particularly for studies focusing on ecosystem-scale carbon metabolism.