Freshwater pools commonly form eccentric crescent patterns in peatlands, an important atmospheric methane (CH4) source, and show an apparent spatial association with eskers in some deglaciated regions. However, the role of underlying permeable glacial deposits such as eskers in regulating hydrogeology, and perhaps even carbon cycling, in peatlands is rarely considered. In this study, ground-penetrating radar imaging and direct coring confirmed that clustered pools coincide with buried esker crests in contact with peat soil in Caribou Bog and Kanokolus Bog in Maine (USA). Hydraulic head and geochemical data combined with lidar indicate vertical water flow from shallow peat toward the permeable esker crests, suggesting enhanced downward transport of labile organic carbon that presumably accelerates rates of methanogenesis in deep peat. Eskers might therefore serve as proxies for enhanced CH4 production in deep peat, as supported by differences in dissolved CH4 profiles depending on proximity to pools. Geographic data compiled from multiple sources suggest that many peatlands with eccentric pools appear to be located proximal to esker systems in Maine and Fennoscandia. These geological factors may be important, previously unrecognized controls on water and the carbon cycle in peatlands.