A series of biogeochemical studies were conducted at the southern summit of Hydrate Ridge, offshore Oregon. Using the submersible DSV Alvin, sediment push cores were collected from two distinct seep environments characterized by the presence of clam fields (CF) or microbial mats (MM) at the sediment-water interface; samples were also collected from a nearby reference site characterized by a barren surface at the sediment-water interface. Sediment samples from each setting were analyzed for the depth distributions of total organic carbon (concentrations, δ13C and Δ14C), total sedimentary nitrogen, and microbial abundance. Pore fluids were extracted and analyzed for sulfate, alkalinity, sulfide, organic carbon, and volatile organic acids. These depth distributions clearly indicate the presence of three distinctive biogeochemical settings in the surface sediments of Hydrate Ridge, and provide the basis for a comparative biogeochemical analysis. Both CF and MM sites display properties indicating enhanced microbial activity in the subsurface, compared with the reference site. MM sites display evidence of net biomass production in the subsurface; however, a loss of sediment nitrogen relative to the reference site indicates that mineralization is also enhanced. Calculations based on the removal of nitrogen indicate that greater than 30% of autochthonous organic material is lost to enhanced mineralization in the top 23 cm of one MM site. An isotope mass balance of sediment-bound organic carbon indicates a mixed source, including methane and allochthonous organic carbon dissolved in the seep fluids. The concentrations of organic carbon dissolved in seep fluids reach values of 22 mM and provide a first indication that advective transport of dissolved organic carbon from great depth may supply an important source of energy and carbon to “methane seep” communities.