High productivity temperate wetlands that accrete peat via belowground biomass (peatlands) may be managed for climate mitigation benefits due to their global distribution and notably negative emissions of atmospheric carbon dioxide (CO₂) through rapid storage of carbon (C) in anoxic soils. Net emissions of additional greenhouse gases (GHG)—methane (CH₄) and nitrous oxide (N₂O)—are more difficult to predict and monitor due to fine-scale temporal and spatial variability, but can potentially reverse the climate mitigation benefits resulting from CO₂ uptake. To support management decisions and modeling, we collected continuous 96 hour high frequency GHG flux data for CO₂, CH₄ and N₂O at multiple scales—static chambers (1 Hz) and eddy covariance (10 Hz)—during peak productivity in a well-studied, impounded coastal peatland in California's Sacramento Delta with high annual rates of C fluxes, sequestering 2065 ± 150 g CO₂ m⁻² y⁻¹ and emitting 64.5 ± 2.4 g CH₄ m⁻² y⁻¹. Chambers (n = 6) showed strong spatial variability along a hydrologic gradient from inlet to interior plots. Daily (24 hour) net CO₂ uptake (NEE) was highest near inlet locations and fell dramatically along the flowpath (−25 to −3.8 to +2.64 g CO₂ m⁻² d⁻¹). In contrast, daily net CH₄ flux increased along the flowpath (0.39 to 0.62 to 0.88 g CH₄ m⁻²d⁻¹), such that sites of high daily CO₂ uptake were sites of low CH₄ emission. Distributed, continuous chamber data exposed five novel insights, and at least two important datagaps for wetland GHG management, including: (1) increasing dominance of CH₄ ebullition fluxes (15%–32% of total) along the flowpath and (2) net negative N₂O flux across all sites as measured during a 4 day period of peak biomass (−1.7 mg N₂O m⁻² d⁻¹; 0.51 g CO₂ eq m⁻² d⁻¹). The net negative emissions of re-established peat-accreting wetlands are notably high, but may be poorly estimated by models that do not consider within-wetland spatial variability due to water flowpaths.