The research presented in this paper focuses on the optimization and modelling of an innovative groundwater extraction system and addresses the challenge of managing the increased groundwater level in Nitra Industrial Park, where the Land Rover Jaguar car manufacturer is located. The primary objective of this research was to determine the optimal pumping rate of the system, ensuring the maintenance of the groundwater level at the required elevation without depleting the surrounding water resources. To achieve this goal, a numerical groundwater modelling approach was utilized, employing the TRIWACO simulation package and the finite element method (FEM). The study involved various simulations under steady and unsteady flow conditions, using hydrological, geological and hydrogeological data, including the results of three proposed pumping tests conducted by INGEO, Ltd. Company, as well as measured groundwater level data from boreholes monitored by the Slovak Hydrometeorological Institute (SHMI). Implementing transient groundwater flow simulations considered the impact of a 1000-year flash flood wave (Q1000). This paper presents results of numerical modelling results, offering insights into maintaining the required groundwater elevation while considering key parameters and uncertainties for design purposes. Additionally, on-site optimization was performed to ensure efficient system operation and minimize associated costs. In conclusion, this research contributes to sustainable groundwater management in the Nitra Industrial Park, addressing the challenge of the increased groundwater level and providing valuable findings to optimize the extraction system’s performance.