Northern peatlands are significant stocks of terrestrial soil carbon, and it has been predicted that warmer temperatures and lower water tables resulting from climate change will convert these ecosystems into sources for atmospheric carbon dioxide (CO2). However, these predictions do not consider the potential for hydrologically induced ecological succession or the spatial variability of carbon accumulation rates between different microforms in peatlands. To address these issues, the vegetation community was described, and the rates of gross ecosystem photosynthesis (GEP), ecosystem respiration (Rtot) and net ecosystem CO2 exchange were determined along poor fen microtopographic gradients at a control site and at a site which experienced a water table drawdown of ∼20 cm 8 years prior to the study (drained). Sampling plots within these sites were classified as microforms of hummocks, lawns, or hollows. The coverage of Sphagnum moss declined on drained hummocks, drained lawns were invaded by sedges, and hollows shifted from open water plots at the control site to Sphagnum‐dominated plots with sparse vascular plant cover at the drained site. As a result, Rtot was significantly greater at the drained site at all microforms while maximum rates of GEP declined at drained hummocks and were enhanced at drained lawns and hollows compared to similar control microforms. These results suggest that predictions about the response of northern peatland carbon exchange to climate change must consider the interaction between ecology and hydrology and the differential responses of microforms related to their initial ecohydrological conditions.