Streams in cultivated lowlands are commonly supersaturated with CO₂ and are a source of CO₂ to the atmosphere. Great uncertainties exist regarding the spatiotemporal variations of CO₂ concentrations and emission rates in stream-lake fluvial networks and small streams with variable plant cover. We studied this variability and the underlying mechanisms in 40 small, high-alkalinity Danish streams, including 5 catchments with lakes. Generally CO₂ concentrations were, on average, 9.2 times those of the atmosphere, declining downstream with rising water temperature, chlorophyll a concentration, and decreasing groundwater inputs. We furthermore observed that the concentrations of CO₂ in stream waters declined at the outlet of lakes to values close to or below air saturation due to phytoplankton uptake and atmospheric loss during the long water retention time in the lakes. Downstream, CO₂ concentrations were observed to decrease in summer and in the afternoons, which indicate plant uptake of CO₂. Sites with deeper water and few plants and low gas transfer velocity retained high CO₂ concentrations. Among 38 fluvial networks where emission could be calculated, it varied 10-fold (0.41–4.06 g C m⁻² d⁻¹), but the overall mean was constrained to a narrow confidence interval (1.75–2.50 g C m⁻² d⁻¹). Our results highlight that a complex of physical, chemical and biological processes cause highly variable carbon dynamics and CO₂ emissions in fluvial networks at local and catchment scales making upscaling challenging.