Ecosystem-atmosphere interactions remain poorly quantified in temperate agroforestry systems despite their potential as nature-based solutions against climate change. In this study, we present CO<sub>2</sub> and H<sub>2</sub>O balances measured with eddy covariance over four pairs of agroforestry with open cropland or grassland systems in northern Germany from 2019 to 2024. Annual sums of net ecosystem CO<sub>2</sub> uptake were generally 1.2- to 4-fold larger at agroforestry sites (average of -113.9 g C m<sup>-2</sup> yr<sup>-1</sup>) compared to open cropland or grassland (average of 20.4 g C m<sup>-2</sup> yr<sup>-1</sup>), while differences in evapotranspiration between systems were comparatively small (averages of 473.7 mm yr<sup>-1 </sup>and 423.5 mm yr<sup>-1</sup>, respectively). Water-use efficiency was thus generally higher at agroforestry, driven primarily by enhanced photosynthetic activity. Site-years with winter crops showed stronger carbon uptake, mostly due to reduced soil emissions in winter. Overall, the inclusion of trees resulted in an extended growing season and reduced sensitivity of these agroecosystems to high air temperature and low soil moisture. Furthermore, although net biome production was positive for most of the site-years, indicating a net carbon release, its magnitude was two or three times higher at open croplands and grassland than agroforestry, indicating stronger carbon losses from the reference systems that always showed a positive balance. These results reveal the potential of agroforestry systems as nature-based solution for climate change mitigation in agriculture, without compromising water availability.