Global warming due to carbon dioxide (CO2) emissions is one of the most important environmental problems in the current century, therefore, there is an urgent need to search for effective eco-friendly strategies to reduce its risks. Biomass of autotrophic microorganisms has been used to reduce carbon dioxide emissions and to produce useful and economically valuable biomass. In the current study, a new strategy was used to improve the CO2 bio-fixation ability of the cyanobacterium S. elongatus, by modifying the design of the closed flat plate photobioreactor by adding mutually inverted U-shaped baffles to increase the efficiency of CO2 retention in the aqueous medium, thus increasing gas availability and utilization during photosynthesis. The results of the saturation and stability experiments indicated that optimal saturation occurred after 60–80 minutes and that the gas stability was for about 2 hours. The results of the bio-fixation experiment showed that the presence of fourteen baffles significantly increased the contact time between the trapped carbon dioxide and the culture medium of S. elongatus, in addition to preventing the rapid release of carbon dioxide from the aqueous medium, thus increasing the availability of carbon dioxide, which led to increasing the biomass productivity of S. elongatus.