Cyanidation wastewater contains heavy metals, including high concentrations of ammonia and free cyanide (CN-). Aerobic growth of Fusarium oxysporum EKT01/02 in synthetic gold mine wastewater under different substrates was examined using biological stoichiometry and thermodynamic models in batch systems. The molecular weight of the dry biomass obtained was 23.03 g/C-mol, 33.14 g C-mol−1, and 27.06 g/C-mol in glucose with ammonia (GA), Beta vulgaris with ammonia (BA), and B. vulgaris with cyanide (BCN) cultures, respectively. The microbial growth model showed the highest biomass yield of 0.69 g dry cell/g substrate in BA cultures. The heat of reaction () and Gibbs energy dissipation per mole of biomass formed () were −652.55/−432.11 kJ/C-mol, −132.59/−471.19 kJ/C-mol, and −370.34/−225.35 kJ/C-mol- for GA, BA, and BCN cultures, respectively. The total Gibbs energy dissipated increased steadily over time and the metabolic rate of the F. oxysporum used was minimally adversely affected by the cyanidation wastewater as shown by the degree of reduction including the respiratory quotient quantified. The F. oxysporum proliferation was determined to be enthalpically driven in the cultures studied. This study revealed that the use of B. vulgaris agro-waste for the bioremediation of cyanidation wastewater is feasible and could engender sustainability of gold mining wastewater treatment processes.