Alkaline conditions induced by algae growth in wastewater stabilization ponds create deprotonated ammonium ions that result in ammonia gas (NH3) volatilization. If algae are utilized to remediate wastewater through uptake of phosphorus, the resulting nitrogen loss will hinder this process because algae generally require a stoichiometric molar ratio of N16P1. Lower ratios of N/P due to loss of ammonia gas will limit the growth and yield of algae, and therefore will reduce phosphorus removal from the water phase into the algae phase. In order to reduce nitrogen loss through volatilization, an ammonium selective zeolite, clinoptilolite, can be used to sequester nitrogen from the water phase as ammonium ion and in a form that is bioavailable for uptake and growth of algae. A novel algae biofilm rotating photo bioreactor (RPB) with clinoptilolite integrated to the outermost surface as the substratum for algae biofilm attachment and growth has been designed, constructed, and tested for ammonium capture and algae biomass production, with simultaneous removal of the algal nutrient phosphorus from water. The clinoptilolite‐based RPB (cRPB) provides algal biomass that can serve as feedstock for biofuel production through uptake of zeolite‐based nitrogen and water phase phosphorus.