Certain embodiments and aspects of the present invention relate to a photobioreactor including photobioreactor units through which a liquid medium stream and a gas stream flow. The photobioreactor units are floated on a body of water such as a pond or a lake. The liquid medium comprises at least one species of phototrophic organism therein. Certain methods of using the photobioreactor system as part of fuel generation system and/or a gas-treatment process or system at least partially remove certain undesirable pollutants from a gas stream. In certain embodiments, the photobioreactor units are formed of flexible, deformable material and are configured to provide a substantially constant thickness of liquid medium. In certain embodiments, a barrier between the photobioreactor unit and the body of water upon which the unit is floated facilitates thermal communication between the liquid medium and the body of water.