This study quantified new biomass production of algae and bacteria in both benthic and pelagic habitats of clear-water lakes to contrast how carbon from the atmosphere and terrestrial sources regulates whole-lake metabolism. We studied four small unproductive lakes in subarctic northern Sweden during one summer season. The production of new biomass in both benthic and pelagic habitats was calculated as the sum of autotrophic production by algae and heterotrophic production by bacteria using allochthonous organic carbon (OC). Whole-lake production of new biomass was dominated by the benthic habitat  (86% ± 4% [mean ± SD]) and by primary production (77% ± 9% Still, heterotrophic bacteria fueled by allochthonous OC constituted a significant portion of the new biomass production in both benthic  (19% ± 11%) and pelagic habitats (51% ± 24%).In addition, overall net production (primary production minus respiration) was close to zero in the benthic habitats but highly negative (−163 ± 81 mg C·m⁻²·d⁻¹)) in pelagic regions of all lakes. We conclude (1) that allochthonous OC supported a significant part of total production of new biomass in both pelagic and benthic habitats, (2) that benthic habitats dominated the whole-lake production of new biomass, and (3) that respiration and net CO2 production dominated the carbon flux of the pelagic habitats and biomass production dominated the benthic carbon flux. Taken together, these findings suggest that previous investigations have greatly underestimated the productivity of clear-water lakes when benthic autotrophic production and metabolism of allochthonous OC have not been measured.