Temperate grasslands are a species-rich ecosystem that may be important in mitigating the increase in atmospheric CO₂. The effect of shrub invasion on CO₂ fluxes in Northern Great Plains grasslands is not known. The objectives of this research were to determine CO₂ and water vapor fluxes over a grazed mixed-grass prairie (prairie site) and a mixed-grass prairie that has extensive invasion of shrubs (shrub prairie site). The Bowen ratio/energy balance (BREB) technique was used to determine CO₂ and water vapor (ET) fluxes during a 4-year period from 1 May to 17 October in 1999, 2000, 2001, and 2002. Aboveground biomass and leaf area index (LAI) were measured about every 21 days throughout the growing season. Peak biomass occurred during July to early August and averaged 1 763 kg · ha⁻¹ for the prairie and 1 808 kg · ha⁻¹ for herbaceous locations in the shrub prairie site. LAI of the herbaceous locations averaged 0.39 for the prairie site and 0.56 for the shrub prairie site. LAI for the shrubs in the shrub prairie site averaged 4.28. Total growing season CO₂ fluxes were similar in prairie and shrub prairie sites, averaging about 350 g CO₂ · m⁻² (positive flux is CO₂ uptake). However, the presence of shrubs altered the seasonal pattern of fluxes. Carbon dioxide fluxes over the shrub prairie site were higher than over the prairie site early in the growing season in May and June, and were often lower than those of the prairie site late in the growing season in August, September, and October. Evapotranspiration rates from May to mid-October were higher in the prairie (521 mm) than the shrub prairie site (461 mm). These results suggest that shrub invasion on Northern Great Plains grasslands does not reduce the potential of grasslands to sequester atmospheric CO₂.