We used input and decomposition data from 14C studies of soils to determine rates of vertical accumulation of moss combined with carbon storage inventories on a sequence of burns to model how carbon accumulates in soils and moss after a stand-killing fire. We used soil drainage—moss associations and soil drainage maps of the old black spruce (OBS) site at the BOREAS northern study area (NSA) to areally weight the contributions of each moderately well drained, feathermoss areas; poorly drained sphagnum—feathermoss areas; and very poorly drained brown moss areas to the carbon storage and flux at the OBS NSA site. On this very old (117 years) complex of black spruce, sphagnum bog veneer, and fen systems we conclude that these systems are likely sequestering 0.01–0.03 kg C m−2 yr−1 at OBS-NSA today. Soil drainage in boreal forests near Thompson, Manitoba, controls carbon storage and flux by controlling moss input and decomposition rates and by controlling through fire the amount and quality of carbon left after burning. On poorly drained soils rich in sphagnum moss, net accumulation and long-term storage of carbon is higher than on better drained soils colonized by feathermosses. The carbon flux of these contrasting ecosystems is best characterized by soil drainage class and stand age, where stands recently burned are net sources of CO2, and maturing stands become increasingly stronger sinks of atmospheric CO2. This approach to measuring carbon storage and flux presents a method of scaling to larger areas using soil drainage, moss cover, and stand age information.