The carbonate chemistry of freshwater systems can range from inorganic carbon‐limited to supersaturated with respect to the atmosphere, and the pH of these systems can vary temporally and spatially from alkaline to acidic. Determining how these heterogeneous systems respond to increases in atmospheric CO2 is critical to understanding global impacts of these changes. Here, we synthesize 22 studies from a variety of systems to explore the effects of elevated CO2 on freshwater chemistry and microalgae, which form the base of autotrophic food webs. Across the variability in freshwater systems, elevated CO2 significantly affected water chemistry by decreasing pH and increasing dissolved inorganic carbon. Microalgae were also affected by elevated CO2 with measured increases in (1) nutrient acquisition through microalgal carbon‐to‐nutrient ratios, (2) photosynthetic activity, and (3) growth. While these effects were measured from controlled experiments, the results indicate a wide range of potential freshwater ecosystem effects from elevated atmospheric CO2. Our synthesis also identified several knowledge gaps. Generally, larger sample sizes and studies of longer duration are needed for more robust analyses and conclusions. Additionally, more field experiments across a range of freshwater ecosystem types and studies involving benthic species and multiple trophic levels are needed to strengthen global predictions across the broad variability found within and among freshwater systems.