Abstract: The inventive technology relates to methods for the algae-based treatment of challenged water. Embodiments of the inventive technology include methods for commercially scalable algal-growth in challenged water. Such methods include, for example a step-wise conditioning process to select and condition algae strains for high growth yields in the presence of challenged water generated from the production of oil and gas or other waste water sources. Such algae-based treatment, in addition to removing harmful chemical compounds from this water may also capture and sequester heavy metal contaminants as well as other compounds for later extraction and processing. The invention also may include embodiments for an algae based desalination system of challenged water, resulting in the production of brine salts and the like. The inventive technology also encompasses an algae-based system to capture and sequester carbon-dioxide from gas and other emissions generated from industrial sources.