A scalable photobioreactor system for efficient production of photosynthetic microorganisms such as microalgae and cyanobacteria is described. In various embodiments, this system may include the use of extended surface area to reduce light intensity and increase photosynthetic efficiency, an external water basin to provide structure and thermal regulation at low cost, flexible plastic or composite panels that are joined together make triangular or other shapes in cross-section when partially submerged in water, use of positive gas buoyancy and pressure to maintain the structural integrity of the photobioreactor chambers and use of structure to optimize distribution of diffuse light. Other embodiments concern air tubes comprised of plastic film at the bottom of each photobioreactor chamber to provide sparging air bubbles to the chamber. The photobioreactor system design also comprises gas exchange, temperature control, air pumping, liquid pumping, filtration, media recycling and harvesting methods. For biofuels production, the photobioreactor system can comprise a separate growth photobioreactor and secondary stress reactor.