High nutrient loading into groundwater and surface water systems has deleterious impacts on the environment, such as eutrophication, decimation of fish populations, and oxygen depletion. Conventional onsite wastewater treatment systems (OWTS) and various waste streams with high ammonium (NH4+) concentrations present a challenge, due the inconsistent performance of environmental biotechnologies aimed at managing nutrients from these sources. Biological nitrogen removal (BNR) is commonly used in batch or packed-bed reactor configurations for nitrogen removal from various waste streams. In recognition of the need for resource recovery, algal photobioreactors are another type of environmental biotechnology with the potential for simultaneously treating wastewater while recovering energy. However, irrespective of the technology adopted, outstanding issues remain that affect the consistent performance of environmental biotechnologies for nitrogen removal and resource recovery. In OWTS, transient loading can lead to inconsistent nitrogen removal efficiency, while the presence of high free ammonia (FA) can exert inhibitory effects on microorganisms that mediate transformation of nitrogen species as well as microalgae that utilize nitrogen. Therefore, to overcome these challenges there have been experimental studies investigating the addition of adsorption and ion exchange (IX) media that can temporarily take up specific nitrogen ions. Bioreactors comprised of microorganisms and adsorption/IX media can attenuate transient loading as well as mitigate inhibitory effects on microorganisms and microalgae; however, the interplay between physicochemical and processes in these systems is not well understood. Therefore, the main objective of this dissertation was to develop theoretical and numerical models that elucidate the complex interactions that influence the fate of chemical species in the bioreactors. To achieve this objective and address the issues related to improving the understanding of the underlying mechanisms occurring within the environmental biotechnologies investigated, the following three research studies were done: (i) experimental and theoretical modeling studies of an IX-assisted nitrification process for treatment of high NH4+ strength wastewater (Chapter 3), (ii) theoretical and numerical modeling of a hybrid algal photosynthesis and ion exchange (HAPIX) process for NH4+ removal and resource recovery (Chapter 4), and (iii) mathematical and numerical modeling of a mixotrophic denitrification process for nitrate (NO3-) removal under transient inflow conditions (Chapter 5). The experimental results for the IX-assisted nitrification process showed that by amending the bioreactor with zeolite, there was a marked increase in the nitrification rate as evidenced by an increase in NO3– production from an initial concentration of 3.7 mg-N L-1 to 160 mg-N L-1. This increase is approximately an order of magnitude greater than the increase in the reactor without chabazite. Therefore, the experimental studies provided support for the hypothesis that IX enhances the nitrification process. To garner further support for the hypothesis and better understand the mechanisms in the bioreactor, a novel mathematical model was developed that mechanistically describes IX kinetics by surface diffusion coupled with a nitrification inhibition model described by the Andrews equation. The agreement between the model and data suggests that the mathematical model developed provides a theoretically sound conceptual understanding of IX-assisted nitrification. A model based on the physics of Fickian diffusion, IX chemistry, and algal growth with co-limiting factors including NH4+, light irradiance, and temperature was developed to describe a batch reactor comprised of microalgae and zeolite. The model can reproduce the temporal history of NH4+ in the reactor as well as the growth of microalgae biomass. The mathematical model developed for the HAPIX process balances between simplicity and accuracy to provide a sound theoretical framework for mechanisms involved. In OWTS, transient inflow conditions have an influence on the performance of environmental biotechnologies for nitrogen removal. Prior experiments have shown that for denitrification, a tire-sulfur hybrid adsorption and denitrification (T-SHAD) bioreactor consistently removes nitrogen under varying influent flow and concentration conditions. To enhance the understanding of the underlying mechanisms in the T-SHAD bioreactor, a mathematical model describing mass transport of NO3- and SO42- in the aqueous phase and mixotrophic denitrification was developed. Additionally, a numerical tool to solve the mathematical model was implemented and compared to previously conducted experiments. Results from the numerical simulations capture the trend of the experimental data showing approximately 90% NO3- -N removal under varying flow conditions. Moreover, the model describes the effluent characteristics of the process showing a transient response in correspondence the changes in fluid velocity. The new tools developed provide new insight into the underlying mechanisms of physical, chemical, and biological processes within these bioreactors. The tools developed in this dissertation have a potential broad impact in environmental biotechnology for wastewater treatment in on-site systems, for treatment of high strength wastewater, and can be extended easily for stormwater management systems aimed at mitigating high nutrient loading to the environment.