The aim of this paper is to propose mathematical models to predict and optimize the cost of wastewater treatment using bacteria and oxygen under fluctuating resource and cultivation conditions. We have thus developed deterministic mathematical models based on dynamic systems and applied optimal control theory to reduce treatment costs. Two wastewater treatment models are proposed: one using only one type of aerobic bacteria, thermophilic bacteria; and the second using two types of aerobic bacteria, thermophilic and mesophilic bacteria. For each model, an optimal control problem is solved and numerical simulations illustrate the theoretical results.