Implementing microalgae biorefinery in arid environments requires utilization of strains that can grow at high temperatures (above 28 °C) and salinity levels (above 30 ppt). In this study, we investigate the newly isolated seawater strain, Synechococcus, native to the United Arab Emirates, and evaluate its value as a perspective organism for cultivation (for fuel and bio-products) in regions with freshwater scarcity. The strain displayed tolerance to a wide range of temperature (22–37 °C) and salinity (20–41 ppt), with maximum biomass concentration of 0.72 g L−1 and a maximum growth rate of 82 mg L−1 d−1 at 25 °C and 33 ppt salinity. Lipids accumulation reached up to 26% of dry weight in nitrogen-depleted conditions (with 1.8 mM of nitrates addition to the media), whereas protein content exceeded 50% dry weight. In this study, harvesting is investigated using three chemical agents: Ferric chloride, sodium hydroxide, and chitosan. Cell disruption is analyzed for four distinct treatments: Enzymatic, alkaline, ultrasonic, and hydrothermal. Among tested methods, flocculation with sodium hydroxide and ultrasonication were found to be the most efficient techniques for harvesting and cell disruption, respectively. The growth characteristics of the local strain and the potential to derive protein and lipids from it makes it a promising biomass in a biorefinery context.