It has become more and more evident that CO<sub>2</sub> emission (<i>F</i><sub>CO<sub>2</sub></sub>) from freshwater systems is an important part in the global carbon cycle. Only few studies addressed the different mechanisms regulating <i>F</i><sub>CO<sub>2</sub></sub> from lotic and lentic systems. In a comparative study we investigated how different biogeochemical and physical factors can affect <i>F</i><sub>CO<sub>2</sub></sub> from streams and reservoirs. We examined the seasonal variability in CO<sub>2</sub> concentrations and emissions from four streams and two pre-dams of a large drinking water reservoir located in the same catchment, and compared them with parallel measured environmental factors. All streams generally were supersaturated with CO<sub>2</sub> over the whole year, while both reservoirs where CO<sub>2</sub> sinks during summer stratification and sources after circulation. <i>F</i><sub>CO<sub>2</sub></sub> from streams ranged from 23 to 355 mmol m<sup>–2</sup> d<sup>–1</sup> and exceeded the fluxes from the reservoirs (–24 to 97 mmol m<sup>–2</sup> d<sup>–1</sup>). Both the generally high piston velocity (<i>k</i>) and CO<sub>2</sub> oversaturation were responsible for the higher <i>F</i><sub>CO<sub>2</sub></sub> from streams in comparison to lakes. In both, streams and reservoirs <i>F</i><sub>CO<sub>2</sub></sub> was mainly controlled by the CO<sub>2</sub> concentration (<i>r</i> = 0.86 for dams, <i>r</i> = 0.90 for streams), which was clearly affected by metabolism and nutrients in both systems. Besides CO<sub>2</sub> concentration, also physical factors control <i>F</i><sub>CO<sub>2</sub></sub> in lakes and streams. During stratification <i>F</i><sub>CO<sub>2</sub></sub> in both pre-dams was controlled by primary production in the epilimnion, which led to a decrease of <i>F</i><sub>CO<sub>2</sub></sub>. During circulation when CO<sub>2</sub> from the hypolimnion was mixed with the epilimnion and the organic matter mineralisation was more relevant, <i>F</i><sub>CO<sub>2</sub></sub> increased. <i>F</i><sub>CO<sub>2</sub></sub> from streams was physically controlled especially by geomorphological and hydrological factors regulating <i>k</i>, which is less relevant in low wind lakes. We developed a schematic model describing the role of the different regulation mechanism on <i>F</i><sub>CO<sub>2</sub></sub> from streams and lakes. <br><br> Taken together, <i>F</i><sub>CO<sub>2</sub></sub> is generally mostly controlled by CO<sub>2</sub> concentration in the surface water. Lake stratification is a very important factor regulating <i>F</i><sub>CO<sub>2</sub></sub> from lakes via controlling CO<sub>2</sub> concentration and metabolism. But <i>F</i><sub>CO<sub>2</sub></sub> in heterotrophic streams is generally higher. The higher <i>k</i> values are responsible for the comparable high <i>F</i><sub>CO<sub>2</sub></sub>. On a Central European landscape scale CO<sub>2</sub> emission from streams was more relevant than the CO<sub>2</sub> flux from standing waters.