The vast majority of research done on constructed treatment wetlands (CTWs) has focused on outdoor installations, with little work done on indoor systems. Previous work on the indoor CTW at the John Heinz National Wildlife Refuge focused on whether the lack of floral diversity in the system would negatively impact its ability to remove various chemical parameters, but despite their great importance in bioremediation the microbial communities in these CTWs have never been studied. In this study, the presence and functionality of ammonia oxidizing bacteria was examined in various points of the treatment system using both culture-dependent and culture-independent DNA-based techniques. In addition, the overall ability of the treatment system to filter out nitrogenous compounds was measured, to demonstrate how its functionality may have changed over the multi-year period since the last study. Water chemical testing revealed that there was a functional shift observed in each section of the treatment system, with much higher levels of ammonium leaving the first aerobic section than before and with the second anaerobic section now eliminating seemingly all forms of inorganic nitrogenous compounds. Despite more levels of ammonium leaving the aerobic section than the anaerobic one, functional assays only indicated ammonia oxidizing activity from the microbial communities isolated from plant roots taken from the aerobic section than the anaerobic one. Metagenomics analysis of the microbial communities isolated from plant roots taken from both sections of the treatment system indicate a dominance of Proteobacteria throughout the entire system, with higher levels of Acidobacteria, Verrucomicrobia, and Planctomycetes in the aerobic section. The higher percentage of Planctomycetes in the aerobic marsh compared to the anaerobic one might be correlated with the brackish water in this component of the CTW, as this condition gives ammonia oxidizing bacteria a competitive advantage over other bacterial types. Furthermore, the absence of Nitrospirae may be correlated with high levels of nitrite in the aerobic section, which would also indicate ammonia oxidation is occurring. Both of these findings suggest that conditions do exist for these bacteria to function well in situ, but some other properties of the marsh may inhibit their activity. For example, the presence of Actinobacteria in the anaerobic marsh could indicate that this section of the CTW Is not fully anaerobic, which may explain why ammonia oxidation occurs there. Due to the great potential of indoor CTWs, and the scarcity of data available on them, more work needs to be done fully understand the microbial dynamics and long-term functionality of these systems.