There is an urgent need to develop ammonia removal treatment systems for municipal and industrial wastewater treatment due to the increasingly stringent ammonia effluent discharge regulations implemented by Canada, the United States, and the European Union. The objective of this dissertation is to develop new understanding and advance the current design and operation of total ammonia nitrogen (TAN) removal via the moving bed biofilm reactor technology (MBBR) for municipal and industrial wastewaters. The first specific objective is to develop a passive, low operationally intensive, efficient and robust design strategy for municipal wastewater treatment to achieve partial nitritation (PN) as a pre-treatment to anammox treatment without using control strategies such as operating at low dissolved oxygen, or the use of inhibitors. This first objective includes developing new knowledge of the biofilm, biomass and microbiome of attached growth PN systems. The second specific objective is to investigate the impact of defining a maximum biofilm thickness, via bio-carrier design, to enhance the effects of free nitrous acid inhibition for PN of municipal wastewaters. The third objective is to investigate the effect of influent copper concentration on nitrifying MBBR systems over long-term operations, to demonstrate the feasibility of the nitrifying MBBR as a solution for TAN removal from gold mining wastewaters. The results pertaining to the first objective, achieved via a study investigating the operation of a nitrifying moving bed biofilm reactor at elevated TAN surface area loading rates (SALRs) of 3, 4, 5, and 6.5 g TAN/m²∙d with the aim of achieving passive PN, demonstrates that operating at a TAN SALR value of 6.5 g TAN/m²∙d can achieve PN without restricting dissolved oxygen or using inhibitors. Operating at a TAN SALR value of 6.5 g TAN/m²∙d achieves a TAN surface area removal rate (SARR) of 3.5 g TAN/m²∙d, and a nitrite accumulation of 99.8% of the oxidized TAN, demonstrating the suppression of nitrite oxidizing bacteria (NOB) activity, while achieving elevated TAN SARR values. At the molecular-scale, there is a statistically significant change in the ammonia oxidizing bacteria (AOB) to NOB ratio from 1:2.6 to 8.7:1 as the TAN SALR increases from 3 to 6.5 g TAN/m²∙d; however, even at a TAN SALR value of 6.5 g TAN/m²∙d there is an NOB abundance of approximately 2%; thus demonstrating that NOB remain present in the biofilm, while their activity is suppressed by operation at elevated TAN SALR values. Furthermore, this system was shown to achieve stable PN consistently for over a period of 10 months of operation, demonstrating a robust, passive, low operational strategy for attached growth PN. The second objective of this dissertation is addressed through a study that compared the carrier design of defined maximal biofilm thickness (z-prototype carrier) to undefined maximal biofilm thickness (chip-prototype carrier) for PN via free nitrous acid inhibition of tertiary, low carbon, municipal wastewaters. The study demonstrates that defined maximal biofilm thickness is a preferred design choice to achieve attached growth PN. The chip-prototype carrier shows biofilm thicknesses and biofilm mass values that are ten-fold higher than the z-prototype carrier, which is shown to contribute to the impact of free nitrous acid on AOB and NOB activities. The z-prototype carrier shows PN is achieved after 3 hours of exposure to free nitrous acid while the chip-prototype carrier does not achieve PN within this same time of exposure. Therefore, the defined maximal biofilm thickness carrier is identified in this research as the preferred design option to achieve attached growth PN for municipal, low carbon, tertiary wastewater treatment. The results of the third objective, achieved via a study investigating the effects of influent copper concentrations on nitrifying MBBR during long term operations to gold mining wastewaters, demonstrates that there is no AOB inhibition in attached growth systems exposed to 0.1, 0.3, 0.45, and 0.6 mg Cu/L for long exposure times. A trend of increasing nitrite accumulation with increasing influent copper concentrations is shown, indicating that NOB inhibition occurs at influent copper concentrations of 0.3 mg Cu/L and greater, with the greatest NOB inhibition observed with an influent copper concentration of 0.6 mg/L. There is no statistically significant difference in biofilm characteristics at the copper concentrations tested; however, there is a trend of increasing biofilm thickness and biofilm roughness with increasing copper concentrations. This study demonstrates the resilience of the nitrifying biofilm to copper inhibition and demonstrates that the nitrifying MBBR is a promising system for removing TAN in mining wastewater in the presence of copper.