The primary objective of the protocol is to establish and develop several scientific methodological procedures applicable to the design and selection of a suitable mine dewatering management plan. A significant challenge and contribution of the research lies in the initial hypothesis, which posits the feasibility of organizing a multidisciplinary team to collaboratively determine the optimal solution for long-term mine dewatering. Protection against groundwater is a highly complex hydrogeological challenge, particularly in mining operations. Mines are inherently dynamic systems, constantly expanding both horizontally and vertically, from the very beginning of mining, also reaching significant depths. Given the inherent uncertainty in geologic systems, such as ore deposits, the entire dewatering process requires continuous “learning” and hierarchical problem-solving. Addressing these complexities involved forming a team of experts, leveraging their knowledge and experience, as well as several methodological procedures based on applied mathematics in geosciences and mining engineering, such as numerical modeling and simulation, fuzzy optimization and decision analysis. These circumstances necessitated continual adjustment to evolving operating conditions and prompted the development of a protocol for effective dewatering planning and mineral ore protection against groundwater. Such a protocol generates alternative mine dewatering solutions and considers their individual characteristics. Additionally, it defines and analyzes multiple criteria for evaluating the solutions and selecting a method that ensures optimal decision-making. The applied methods constitute a holistic system, represented by a single protocol, which includes an interdisciplinary approach to creating sustainable groundwater management strategies.