Methane is the main end product of anaerobic degradation in freshwater sediments. The flux of methane from the sediment into the water column, and possible methane oxidation at the sediment surface, can be estimated on the basis of its distribution in the sediment and the overlying water. Nonetheless, the quantification of methane in sediments at high spatial resolution is difficult, owing to its chemical inertia. In this study, we describe the improvement of a diffusion-based methane sensor and its application in freshwater sediment cores. The sensor consists of a steel cannula with small openings, which are covered by thin silicone tubing. Methane diffuses into the cannula and is flushed directly to a flame ionization detector for quantification. With this sensor, methane profiles in freshwater sediment can be measured at high spatial (1.5 mm) and temporal (3 minutes per measurement) resolution. The detection limit was 2 μmol L-1. The relative accuracy of the sensor was ± 15% with a precision of ± 7.5%. Analysis of fine-scale methane profiles in littoral and profundal sediments of Lake Constance indicate that owing to structural inhomogeneities and temporal changes a high-resolution analysis is required to allow exact calculations of diffusive fluxes and turnover rates of methane.