The surface pattern of vegetation influences the composition and humification of peat laid down during the development of a bog, producing a subsurface hydrological structure that is expected to affect both the rate and pattern of water flow. Subsurface peat structures are routinely derived from the inspection of peat cores. However, logistical limits on the number of cores that can be collected means that the horizontal extent of these structures must be inferred. We consider whether subsurface patterns in peat physical properties can be mapped in detail over large areas with ground-penetrating radar (GPR) and complex conductivity by comparing geophysical measurements with peat core data along a 36 m transect through different microhabitats at Caribou Bog, Maine. The geophysical methods show promise. Peat horizons produced radar reflections because of changes in the volumetric moisture content. Although these reflections could not be directly correlated with the peat core data, they were related to the depth-averaged peat properties which varied markedly between the microhabitats. Well-decomposed peat below a hollow was characterized by a discontinuous sequence of chaotic wavy reflections, while distinct layering of the peat below an area of hummocks coincided with a pattern of parallel planar reflections. The complex conductivity survey showed spatial variation in the real and imaginary conductivities which resulted from changes in the pore water conductivity; peat structures may also have influenced the spatial pattern in the complex conductivity. The GPR and complex conductivity surveys enabled the developmental history of the different microhabitats along the studied transect to be inferred.