Headwater stream networks contribute substantially to the global carbon dioxide terrestrial flux because of high turbulence and coupling with terrestrial environments. Heterogeneity within headwater stream networks, both spatially and temporally, makes measuring and upscaling these emissions challenging because measurements of carbon dioxide in streams are often limited to a few monitoring points. We modified a stream network model to reflect real measurements made under base flow and high flow conditions at Martha Creek in Stabler, WA in the US Pacific Northwest. We found that under high flow conditions, the stream network had much greater total carbon emissions than during low flow conditions (1.22 Mg C day−1 vs. 0.034 Mg C day−1). We attribute this increase to a larger overall stream network area (0.04 vs. 0.01 km2) and discharge (1.9 m3 s−1 vs. 0.005 m3 s−1) in November versus August. Our results demonstrate the need to understand the nonperennial stream reaches when calculating carbon emissions. We compared the stream network emissions with the terrestrial net ecosystem exchange (NEE) estimated by local eddy covariance measurements per watershed area (−5.5 Mg C day−1 in August and −2.2 Mg C day−1 in November). Daily stream emissions in November accounted for a much larger percentage of NEE than in August (54% vs. 0.62%). We concluded that the stream network can emit a large percentage of the forest NEE in the winter months, and annual estimates of stream network emissions must consider the flow regime throughout the year.