Ten algae species were analyzed by comparing their growth in specific hypersaline industrial wastewater. It was a by-product of fertilizer production which was released by K + S Aktiengesellschaft, Germany. Due to processing, brine water contains a high amount of salts (200 g L−1). A successful algal biotechnology mainly depends on choosing and screening the adequate algae for a specific application along with the design of optimal culture conditions with comparable photo bioreactor technologies. Therefore, a high throughput screening technology was developed. In comparison to glass flasks or flat panel reactors this system was eligible for screening applications because of disposable characteristics and the equability of each culture tube. Dunaliella salina, Tetraselmis tetrathele, and Nannochloropsis salina grew in the presence of hypersaline wastewater where T. tetrathele grew best to a wastewater concentration of 75% by salt shock experiments. D. salina tolerates a wastewater level up to 80% by gradual increase. Intracellular ion contents of lyophilized algae samples were measured. They feature special transporter to either exclude ions, i.e., sodium from the cell, or to include ions like potassium and magnesium in order to secure functionality of sensitive enzymes. Under saline stress conditions these transport systems as well as metabolic pathways leading to the production of compatible osmolytes could be induced. Stress tolerance mechanisms developed in initially unstressed culture either by stepwise adaptation or by shock exposure to harsh salt condition. For this reason a feasible mass production in industrial hypersaline wastewater was possible.