Peatlands often show patterns of small-scale topographic self-organization, such as hummock and hollow assemblages. When attempting to characterize peatland pore-water quality, little attention is typically paid to the micro-site characteristics of the sampling location, or only one microtopographical form is sampled for consistency. However, no information exists regarding whether or not these microtopographic landforms exert a direct influence over, or are influenced by, the chemistry of peat pore waters beneath them. As part of a larger study examining the role of peatlands in catchment-scale methylmercury cycling, the pore waters beneath several peatland microtopographical landforms were sampled for methylmercury. Pore-water methylmercury (MeHg) concentrations at the water table followed the trend: Shallow Hollow > Lawn > Hummock > Deep Hollow, with the shallow hollows having pore-water methylmercury concentrations over 3.5 times higher than that found in deep hollows. There was no significant difference in MeHg concentrations in pore waters from −25 cm. More detailed profiles of MeHg, sulfate and DOC concentrations, and pH in a poor fen shallow and deep hollow and a raised bog hollow show strong differences in pore-water solute chemistry, suggesting a complex interplay among hydrology, biogeochemistry, and microtopography. Evidence of wide variation in pore-water quality between sites and over time has significant implications for the sampling approaches used to characterize peatland pore-water chemistry.