Agricultural waste accounts for 10% of annual greenhouse gas emissions in the United States and increases by at least 5% annually due to population growth. The rise in agricultural waste makes it imperative to improve the management and recovery of value-added products of agricultural residues. Current strategies to treat and valorize agricultural wastes involve using thermochemical or biochemical processes to recover energy-rich, value-added products from residues. Thermochemical processes, such as pyrolysis and hydrothermal treatment (HTP) require shorter residence times than biochemical processes and have higher conversion efficiencies. Yet thermochemical conversions have their own set of obstacles. The bio-oil produced from pyrolysis is often highly oxygenated, which reduces its combustion quality, restricting this product as a cleaner commercial alternative for oil-based fuels. Incorporating both processes into a multi-step treatment pathway may improve the final products of thermochemical treatment. In this work, a hydrothermal treatment step before pyrolysis, co-treating plastic and lignocellulosic biomass, was incorporated to investigate how the devolatization of the feedstock in HTP improves the resulting products of pyrolysis. This study demonstrated that the addition of co-HTP before pyrolysis significantly reduced the oxygen content in the bio-oil. While HTP is a beneficial step in the bio-oil upgrading process, it produces an aqueous waste stream, referred to as the aqueous phase (AP), that is rich in contaminants and nutrients, such as nitrogen and phosphorus. Ammonia nitrogen is of particular interest due to its demand in the agriculture and chemical industries, while acting as an environmental contaminant in water streams. Removal of ammonia from the HTP AP using adsorption on natural zeolites was investigated in this work. Previous studies have shown the selective adsorption of ammonia using a natural zeolite, clinoptilolite, was suitable for ammonia adsorption from water, due to its anionic tetrahedral aluminum-silicate framework. In this study, we evaluated clinoptilolite’s selectivity in a model solution representative of compounds commonly found in the HTP AP. Eight different concentrations of ammonia in the presence of these organic acids, phenolics, and nitrogen heterocyclics were tested to determine if any of these compounds interfered with adsorption and if it was possible to adsorb ammonia selectively. Equilibrium and kinetics isotherm studies indicated that the addition of these compounds did not affect the ammonia adsorption capacity in the model solution, suggesting that both physical and chemical mechanisms, predominantly chemical due to ion exchange, contribute to selective adsorption. The findings of this work provide insights into the potential for nutrient recovery from the HTL waste stream and the incorporation of hydrothermal processes and pyrolysis to improve the production and recovery of valuable products from agricultural residues.