Carbon mass balance studies of 20 small, forested catchments and seven lakes on the Precambrian Shield in central Ontario during a 12-year period have shown that most carbon in the study lakes is derived from terrestrial sources, primarily peatlands, and that carbon retained by lakes (total inputs less loss via outflow from the lake) is partitioned between lake sediments and the atmosphere. The partitioning of retained carbon is a function of lake alkalinity: the ratio of evaded/sediment carbon increases with decreasing alkalinity. These carbon flux relationships were applied to the global boreal forest biome to evaluate the role of aquatic systems with respect to carbon fluxes and pools within the biome. We calculate that approximately 66 Tg of organic and inorganic carbon are exported annually from the boreal forest biome to adjacent surface waters of which 14 to 36 Tg reach coastal waters. The remainder is either evaded to the atmosphere (12 to 21 Tg yr−1) or stored in lake sediments (18 to 31 Tg yr−1). Approximately 120 Pg of carbon may be stored in boreal lake sediments, a conservative estimate based on an accumulation period of 5,000 years and a size comparable to recent boreal pool estimates of 419 Pg for peatlands and 64 Pg for plant biomass. Hence the amount of total carbon stored in the boreal forest biome may be significantly larger because of storage in lake sediments.