This study compares eddy-covariance measurements of carbon dioxide fluxes at six northern temperate and boreal peatland sites in Canada and the northern United States of America, representing both bogs and fens. The two peatland types had opposite responses of gross ecosystem photosynthesis (GEP) and ecosystem respiration (ER) to inter-annual fluctuations in water table level. At fens, wetter conditions were correlated with lower GEP and ER, while at bogs wetter conditions were correlated with higher GEP and ER. We hypothesize that these contrasting responses are due to differences in the relative contributions of vascular plants and mosses. The coherence of our results between sites representing a range of average environmental conditions indicates ecosystem-scale differences in resilience to hydrological changes that should be taken into account when considering the future of peatland ecosystem services such as carbon sequestration under changing environmental conditions.