Elevated atmospheric carbon dioxide (eCO2) has been shown to have a variety of ecosystem-level effects in terrestrial systems, but few studies have examined how eCO2 might affect aquatic habitats. This limits broad generalizations about the effects of a changing climate across biomes. To broaden this generalization, we used free air CO2 enrichment to compare effects of eCO2 (i.e., double ambient ∼720 ppm) relative to ambient CO2 (aCO2∼360 ppm) on several ecosystem properties and functions in large, outdoor, experimental mesocosms that mimicked shallow sand-bottom prairie streams. In general, we showed that eCO2 had strong bottom-up effects on stream autotrophs, which moved through the food web and indirectly affected consumer trophic levels. These general effects were likely mediated by differential CO2 limitation between the eCO2 and aCO2 treatments. For example, we found that eCO2 decreased water-column pH and increased dissolved CO2 in the mesocosms, reducing CO2-limitation at times of intense primary production (PP). At these times, PP of benthic algae was about two times greater in the eCO2 treatment than aCO2 treatment. Elevated PP enhanced the rate of carbon assimilation relative to nutrient uptake, which reduced algae quality in the eCO2 treatment. We predicted that reduced algae quality would negatively affect benthic invertebrates. However, density, biomass and average individual size of benthic invertebrates increased in the eCO2 treatment relative to aCO2 treatment. This suggested that total PP was a more important regulator of secondary production than food quality in our experiment. This study broadens generalizations about ecosystem-level effects of a changing climate by providing some of the first evidence that the global increase in atmospheric CO2 might affect autotrophs and consumers in small stream ecosystems throughout the southern Great Plains and Gulf Coastal slope of North America.