To elucidate the roles of hydrology and vegetation in below ground carbon cycling within peatlands, radiocarbon values were obtained for pore water dissolved organic carbon (DOC), dissolved inorganic carbon (DIC), CH4, and peat from the Glacial Lake Agassiz peatland. The major implication of this work is that the rate of microbial respiration within a peat column is greater than the peat decomposition rate. The radiocarbon content of DOC at both bog and fen was enriched relative to solid-phase peat by ∼150-300‰ consistent with the advection of recently photosynthesized DOC downward into the peat column. Fen Δ14C values for DIC and CH4 closely track the Δ14C of pore water DOC at depth, indicating that this recent plant production was the predominant substrate for microbial respiration. Aceticlastic methanogenesis apparently dominated the upper third of the peat column (α = 1.05), shifting toward CO2 reduction with depth (1.05 < α < 1.08). Upwelling groundwater contributed as much as 15% of the DIC to the bulk DIC pool at depth in the fen. The similarity of Δ14C values for DIC and CH4 suggests that methanogens utilized DIC from this source as well as DIC produced in situ. Bog Δ14C values for pore water DIC and CH4 differ by ≤ 15‰ at all depths and are depleted in 14C relative to DOC by ∼100‰, suggesting microbial utilization of a mixture of older and modern substrates. CO2 reduction was the primary pathway for methanogenesis at all depths in the bog (α = 1.08), and groundwater influence on bulk DIC was negligible. For both sites, Δ14C−DIC and Δ14C−CH4 are approximately equal at depths where stable isotope data indicate a predominance of CO2 reduction and dissimilar when acetate fermentation is indicated.