Metabolism is one of the most fundamental ecosystem processes, but the drivers of variation in metabolic rates among lakes dominated by benthic primary producers remain poorly constrained. Here, we report the magnitudes and potential drivers of whole-lake metabolism across 43 Swedish arctic–alpine lakes, based on the free-water diel oxygen technique with sondes deployed during the open-water season near the surface and bottom of the lakes. Gross primary production (GPP) and ecosystem respiration (R) were strongly coupled and ranged from 0.06 to 0.45 mg and 0.05 to 0.43 mg L⁻¹ d⁻¹ among lakes. On average, GPP and R decreased eightfold from relatively shallow to deep lakes (mean depth 0.5–10.9 m) and twofold from concave to convex lakes (mean depth: maximum depth 0.2–0.5). We attribute this to light limitation and shape-specific sensitivity of benthic GPP to disturbance by lake ice. Net ecosystem production (GPP-R) ranged from −0.09 to 0.14 mg L⁻¹ d⁻¹ and switched, on average, from positive to negative towards deeper lakes and lakes richer in dissolved organic carbon (DOC; 0.5–7.4 mg DOC L⁻¹). Uncertainties in metabolism estimates were high (around one and three times mean R and GPP), especially in deep lakes with low insulation and diurnally variable wind speed. Our results confirm the role of DOC in stimulating net heterotrophy and highlight novel effects of lake shape on productivity in benthic-dominated lake ecosystems and its response to changes in lake ice cover.