Open-water perennial pools are common natural features of peatlands globally, and peatland restoration often results in new pool creation, yet the concentrations of different forms of aquatic carbon (C) in natural and artificial restoration pools are not well studied. We compared carbon concentrations in both natural pools and restoration pools (4–15 years old) on three blanket peatlands in northern Scotland. At all sites, restoration pools were more acidic and had mean dissolved organic carbon (DOC) concentrations in restoration pools of 23, 22, and 31 mg L−1 compared with natural pool means of 11, 11 and 15 mg L−1 respectively across the three sites. Restoration pools had a greater fulvic acid prevalence than the natural pools and their DOC was more aromatic. Restoration pools were supersaturated with dissolved CO2 at around 10 times atmospheric levels, whereas for natural pools, CO2 concentrations were just above atmospheric levels. Dissolved CH4 concentrations were not different between pool types, but were ~200 times higher than atmospheric levels. Regular sampling at one of the peatland sites over 2.5 years showed that particulate organic carbon (POC) concentrations were generally below 7 mg L−1 except during the warm, dry summer of 2013. At this regularly-sampled site, natural pools were found to process DOC so that mean pool outflow concentrations in overland flow were significantly lower than mean inflow DOC concentrations. Such an effect was not found for the restoration pools. Soil solution and pool water chemistry, and relationships between DOC and CO2 concentrations suggest that different processes are controlling the transformation of C, and therefore the form and amount of C, in natural pools compared to restoration pools.