This dataset includes greenhouse gas flux measurements and sediment bubble/root structure data from a freshwater microcosm experiment conducted at Radboud University, the Netherlands (April–June 2023). Thirty microcosms representing five macrophyte species and a non-vegetated control were monitored weekly for methane (CH₄) and carbon dioxide (CO₂) emissions. CH₄ diffusion and ebullition were quantified separately using flux chambers and bubble traps. A novel sediment scanning method was used to visualize and quantify root volume and gas bubbles. Data include raw and processed flux values, image-derived measurements, and a custom ImageJ script for semi-automatic annotation.