Abstract Humans are altering coastal regions directly (land‐use, drainage) and indirectly (climate change). Alterations potentially create positive climate feedback loops by enhancing production and emission of aquatic greenhouse gases (GHGs) CO2, N2O, and CH4. We tested this hypothesis by measuring dissolved CO2, N2O, and CH4 concentrations across the anthropogenic aquatic continuum (farm ponds, ditches, irrigation drains, streams, tidal rivers, and estuaries) and continuously during a winter storm. Combining measurements with hydrodynamic modeling enabled us to parameterize physical gas transfer uncertainties, revealing artificial waterways contributed disproportionately to emissions. Ditches and drains cover 5% of water surface area but produced >50% of emissions (2–11 Mmol d−1 CO2‐equivalents). But storms inverted this pattern by increasing estuary emissions 16‐fold (5.0 Mmol d−1 CO2‐equivalent), suggesting storm patterns could control both sources and magnitudes of aquatic GHG emissions. Findings show overlooked artificial drains and hard‐to‐measure storms will increasingly define the aquatic offsets of landscape carbon budgets.

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