As part of the 2007 Marnaut cruise in the Sea of Marmara, an investigation of the pore fluid chemistry of sites along the Main Marmara Fault zone was conducted. The goal was to define the spatial relationship between active faults and fluid outlets and to determine the sources and evolution of the fluids. Sites included basin bounding transtensional faults and strike-slip faults cutting through the topographic highs. The basin pore fluids are dominated by simple mixing of bottom water with a brackish, low-density Pleistocene Lake Marmara end-member that is advecting buoyantly and/or diffusing from a relatively shallow depth. This mix is overprinted by shallow redox reactions and carbonate precipitation. The ridge sites are more complex with evidence for deep-sourced fluids including thermogenic gas and evidence for both silicate and carbonate diagenetic processes. One site on the Western High displayed two mound structures that appear to be chemoherms atop a deep-seated fluid conduit. The fluids being expelled are brines of up to twice seawater salinity with an exotic fluid chemistry extremely high in Li, Sr, and Ba. Oil globules were observed both at the surface and in cores, and type II gas hydrates of thermogenic origin were recovered. Hydrate formation near the seafloor contributes to increase brine concentration but cannot explain their chemical composition, which appears to be influenced by diagenetic reactions at temperatures of 75°C–150°C. Hence, a potential source for fluids at this site is the water associated with the reservoir from which the gas and oil is seeping, which has been shown to be related to the Thrace Basin hydrocarbon system. Our work shows that submerged continental transform plate boundaries can be hydrologically active and exhibit a diversity of sources and processes.