I investigated the effects of multi-decadal water table drawdown on carbon (C) exchange, as well as functional relationships between C fluxes and environmental controls, in a boreal rich fen. Drainage increased ecosystem respiration of CO2 and decreased CH4 fluxes, but did not affect understory primary productivity. Drainage altered plant responses to light availability, as well as the responses of ecosystem respiration and CH4 flux to water table position. In a laboratory experiment, I found that drainage reduced potential CO2 and CH4 fluxes suggestive of decreased peat substrate quality. Together, these results indicate that long-term drying increases C losses and that both environmental conditions and substrate quality influenced C fluxes post-drainage. My findings suggest that C losses from increased ecosystem respiration may not be mitigated by increases in plant productivity or decreases in substrate quality, and that long-term drainage reduced C storage capacity in this boreal fen.