Expanding environmentally friendly and sustainable aquaculture systems is needed to reduce fishing pressure on declining wild fish populations and meet the ever-increasing demand for safe and sustainable seafood. Conventional aquaculture is challenged by high water demand, pollutant discharge, biosecurity, and disease. Marine or salt-water recirculating aquaculture systems (RAS) have the potential to address many of these challenges; however, these RAS systems face obstacles that need to be addressed, such as high energy demand, discharge of saline water and organic salty solids, and the lack of a standardized RAS filtration system. Improving the economic viability and sustainability of zero-discharge marine RAS led Mote Aquaculture Research Park (Mote) scientists to develop a marine aquaponics or Integrated Multi-Trophic Aquaculture (IMTA) system. This IMTA system was engineered to efficiently use nutrients, water and conserve energy to produce marine fish and edible sea vegetables. Mote, in partnership with the National Mariculture Center (NMC) in Israel, the University of South Florida’s College of Engineering (USF) and Auburn University are now exploring opportunities to combine aquaculture biofilters in IMTA systems to recover excess nutrients, produce additional end-products and increase revenue. Incorporation of periphyton biofilters into Mote’s IMTA not only improved water quality by reducing excess nitrogen and carbon dioxide, but produced dissolved oxygen and repurposed nutrients that can be harvested and used as a potential ingredient for fish feeds. In addition, some nutrients removed from the water can be reclaimed and harvested monthly. Analysis of the microbiome in the periphyton community revealed the presence of denitrifiers, ammonia-oxidizing microbes, nitrite-oxidizing microbes, and valuable algae such as Chlorella. Results from trials evaluating different aquaculture biofilter combinations with halophytes, periphyton and moving bed biofilm reactors will be presented. The goal of this research is to develop a pragmatic system that can be managed by family or farmer-owned cooperatives, to supply communities with locally produced fresh seafood and provide expanded job opportunities in rural and urban communities.