A one‐dimensional reaction‐transport model is used to investigate the dynamics of methane gas in coastal sediments in response to intra‐annual variations in temperature and pressure. The model is applied to data from two shallow water sites in Eckernforde Bay (Germany) characterized by low and high rates of upward fluid advection. At both sites, organic matter is buried below the sulfate‐reducing zone to the methanogenic zone at sufficiently high rates to allow supersaturation of the pore water with dissolved methane and to form a free methane gas phase. The methane solubility concentration varies by similar magnitudes at both study sites in response to bottom water temperature changes and leads to pronounced peaks in the gas volume fraction in autumn when the methanic zone temperature is at a maximum. Yearly hydrostatic pressure variations have comparatively negligible effects on methane solubility. Field data suggest that no free gas escapes to the water column at any time of the year. Although the existence of gas migration cannot be substantiated by direct observation, a speculative mechanism for slow moving gas is proposed here. The model results reveal that free gas migrating upward into the undersaturated pore water will completely dissolve and subsequently be consumed above the free gas depth (FGD) by anaerobic oxidation of methane (AOM). This microbially mediated process maintains methane undersaturation above the FGD. Although the complexities introduced by seasonal changes in temperature lead to different seasonal trends for the depth‐integrated AOM rates and the FGD, both sites adhere to previously developed prognostic indicators for methane fluxes based on the FGD.