Ground penetrating radar (GPR) was used to determine peat basin geometry and the spatial distribution of free-phase biogenic gasses in two separate units of a northern peatland (Central and Southern Unit of Caribou Bog, Maine). The Central Unit is characterized by a deep basin structure (15 m maximum depth) and a raised (eccentric) bog topographic profile (up to 2 m topographic variation). Here numerous regions of electromagnetic (EM) wave scattering are considered diagnostic of the presence of extensive free-phase biogenic gas. In contrast, the Southern Unit is shallower (8 m maximum depth) and has a slightly convex upwards bog profile (less than 1 m topographic variation), and areas of EM wave scattering are notably absent. The biogenic gas zones interpreted from GPR in the Central Unit are associated with: (1) wooded heath vegetation at the surface, (2) open pools at the surface, (3) high water table elevations near the center of the basin, and (4) a region of overpressure (at approximately 5 m depth) immediately below the zone of free-phase gas accumulation. The latter suggests (1) a transient pressure head associated with low hydraulic conductivity resulting from the biogenic gasses themselves or confining layers in the peat that restrict both gas release and groundwater flow and/or (2) overpressure in the peat column as a result of the gas buildup itself. In contrast, the Southern Unit, where zones of EM scattering are absent, is characterized by: (1) predominantly shrub vegetation, (2) a lack of open pools, (3) only minor variations (less than 1 m) in water table elevation throughout the entire unit; and (4) generally upward groundwater flow throughout the basin. The results illustrate the nonuniformity of free-phase biogenic gas distribution at the peat basin scale and provide insights into the processes and controls associated with CH4 and CO2 accumulation in peatlands.