A unique aqueous silica removal process using naturally occurring diatoms for water reuse and desalination is described. Several strains of brackish water diatoms have been isolated and tested. Among them Pseudostaurosira and Nitzschia species showed promise. Reverse osmosis (RO) concentrate samples from two full-scale advanced water purification facilities and one brackish groundwater RO plant in Southern California have been successfully treated by this process. This new photobiological process could remove aqueous silica, as well as phosphate, ammonia, nitrate, calcium, iron and manganese very effectively. Under non-optimized conditions, 95% of 78 mg·L−1 reactive silica in an RO concentrate sample could be removed within 72 hours. In most cases, addition of nutrients was not necessary because the RO concentrate typically contains sufficient concentrations of macronutrients derived from the source water (i.e., treated wastewater and brackish groundwater). Preliminary characterization of organics indicated that there was no major generation of dissolved organics, which could potentially foul membranes in the subsequent RO process. This new algal process has a strong potential for its application in desalination and water reuse in the United States and around the world.