The factors controlling fluid emission dynamics at ocean margins are poorly understood. In particular, there are significant uncertainties on how fluid seepage at cold seeps may have responded to abrupt environmental changes in the geological past. This study reports on a detailed geochemical investigation of seafloor carbonate crusts sampled at cold seeps along the submerged part of the North Anatolian Fault system in the Sea of Marmara - an inland sea, which has experienced major paleo-environmental changes over the last deglaciation period. We also analyzed a series of authigenic carbonate concretions recovered from two sediment cores at the Western-High ridge, an active fluid venting area. The ages of seafloor carbonate crusts derived from isochron U-Th dating cover the last 7 kyr, suggesting that fluid activity along the fault system remained continuous over that time interval. In the sediment cores, carbonate concretions are concentrated at the lacustrine-to-marine transition, which corresponds to the period when Mediterranean waters flowed into the Marmara Basin about 12-14 kyr ago. U-Th isotopic data indicate that most of these concretions formed later during the Holocene, around 9-10 kyr ago, a period coinciding with an important anoxic event that led to the deposition of a sapropel layer in the Sea of Marmara. Based upon these results, we suggest that the absence of carbonate concretions in the lacustrine sediment unit indicates that dissolved sulfate concentrations in the Marmara lake pore waters during glacial time were too low to promote significant anaerobic methane oxidation, thereby preventing sedimentary carbonate authigenesis. In contrast, the progressive inflow of Mediterranean waters into the glacial Marmara lake after 15 ka provided a source of dissolved sulfate that allowed anaerobic oxidation of methane to proceed within the anoxic sediment. Importantly, the synchronism between the main phase of authigenic carbonate precipitation at the studied sites (average 9.4 +/- 1.8 ka, n = 16) and the regional anoxic sapropel event support the idea that the drop in bottom water dissolved oxygen content was probably a key factor to enhance microbial activity and associated carbonate precipitation at that time. Overall, these results provide straightforward evidence that fluid emission dynamics and hydrocarbon oxidation at cold seeps can be directly related to changing environmental conditions through time.