Today, wastewater treatment projects are very important to preserve human health and the terrestrial and aquatic ecosystems. The valuation of these projects presents some difficulties related to the uncertainty of wastewater flows over time and the operational flexibilities that influences their performance. This paper aims to provide a valuation methodology of wastewater treatment projects that can consider the stochastic nature of the wastewater volume, the operational flexibility to expand the project, and the possibility of turning off the system when the wastewater volume is too low to avoid financial losses. To pursue this goal, we apply a Real Options Approach (ROA) fitted for the characteristics of the wastewater volume in an agricultural firm, such as its evolution through a standard Brownian motion to which it is applied a seasonality component referred to the availability of fruits and vegetables in certain months. We also propose a case study related to a wastewater treatment project carried out by the Rosso Gargano Company in southern Italy.