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Abstract The temporal structures of gross primary production (GPP) and ecosystem respiration (ER) vary across time scales in response to complex interactions among dynamic drivers (e.g., flow, light, temperature, organic matter supply). To explore emergent patterns of river metabolic variation, we applied frequency‐domain analysis to multiyear records of metabolism across 87 US rivers. We observed a dominant annual periodicity in metabolic variation and universal fractal scaling (i.e., power spectral density inversely correlated with frequency) at subannual frequencies, suggesting these are foundational temporal structures of river metabolic regimes. Frequency‐domain patterns of river metabolism aligned best with drivers related to energy inputs: benthic light for GPP and GPP for ER. Simple river metabolism models captured frequency‐domain patterns when parameterized with appropriate energy inputs but neglecting temperature controls. These results imply that temporal variation of energy supply imprints directly on metabolic signals and that frequency‐domain patterns provide benchmark properties to predict river metabolic regimes.