Recirculating aquaculture systems (RAS) produce aquaculture products on land with minimal discharge of waste products and minimal water loss. High costs associated with waste treatment for RAS have triggered the growth of integrated aquaculture systems (IAS) which incorporate macrophytes (aquatic plants) into the treatment train. The objective of this research was to examine a pilot scale inland marine IAS with three different methods for solids treatment: a sand filter followed by a plant bed, only a plant bed, and geotextile bags. Florida Pompano (Trachinotus carolinus) were grown along with Smooth Cordgrass (Spartina alterniflora), Black Needle Rush (Juncus romerianus), and Red Mangrove (Rhizophora mangle). Between May 2011 and April 2012, water quality was tested at seven points located throughout the IAS for total suspended solids (TSS), chemical oxygen demand (COD), total nitrogen (TN), ammonium (NH4+), nitrate (NO3-), total phosphorus (TP), and orthophosphate (PO43-) concentrations every 4 to 6 weeks. Plant and soil samples were collected three times and analyzed for total nitrogen and total phosphorus. A statistically significant difference in the effluent concentrations for the three treatments was not found; however, due to the recombination of effluent from the solid treatments and the variability inherent in a pilot scale system it was difficult to isolate the individual efficiencies of each treatment. Therefore, on average the complete system achieved COD and TSS removal efficiency of 59% and 88%, respectively and TN and TP removal efficiency of 48% and 19%, respectively. Nutrient uptake by plants did not vary significantly between the plant beds. In general, the system provided sufficient nutrient removal for safe fish production, and the fish provided enough nutrients for ample plant growth.