Due to increasing energy demands, fossil fuel combustion has grown significantly over the last decades. Concomitantly, the biosphere’s atmospheric component has undergone drastic alterations attributed largely to anthropogenic releases of greenhouse gases (GHGs) and combustive aerosols. Carbon-dioxide and Oxides of nitrogen (NOx) have received much attention due to their abilities to alter rainfall chemistry, augment atmospheric fertilization, and decrease albedo. As such, capturing these damaging compounds is now a priority. One approach is via microalgae grown in tandem with processes liberating these nutrients since many are essential in autotrophic metabolism. Culturing algae in open raceway ponds (ORP’s) has its disadvantages, as these systems are subjected to high evaporation and contamination rates. Closed photobioreactors (PBR’s) are now favored because of increased environmental control, but inefficiencies in heat dissipation and light penetration still persist. These shortcomings clearly indicate a need for optimizations to increase algal biomass, and therefore, the nutrient capturing and recycling capabilities of these systems. This research tested the hypothesis that spectral filtering and PBR design can increase efficiency and remediation. To accomplish this, low cost optical filters were first evaluated for their effects on biomass and culture temperature of some microalgae, including Chlamydomonas reinhardtii and Scenedesmus dimorphus. Based on these initial tests, a PBR was fabricated and fertilized by flue from a steam boiler. The system was then evaluated for its effects on efflux nutrient concentrations versus non PBR cycles. Initial indications revealed that both filtering and PBR design could decrease efflux nutrients and culture temperature, thus improving performance.