Dewatering and groundwater control are activities continuously implemented and monitored throughout the duration of underground mining or open pit projects. The proper and efficient implementation of these activities depends on large hydrogeological studies, for assessing the most appropriate control systems. The demand for technical and economic efficiency of these processes requires three-dimensional flow numerical analysis of the entire study area, characterized by deep and complex stratifications of permeable materials below the water table, as usually cover mining projects, where analytical solutions cannot be applied. The present research contributes to a better understanding of the numerical formulations that represent the behavior of groundwater flow via two case studies—the first in an underground mine and the second in a surface mine. In the case of the underground mine, 1D discrete elements were incorporated within a finite-three dimensional model in order to represent preferential flow paths. The advantages of incorporating such features explicitly to quantify the flow passing through them, that feed the mine through direct connections with an adjacent river, were discussed. The use of discrete elements allows for a more realistic representation of the hydrogeological environment and, at the same time, a more refined assessment of the effects on the behavior of groundwater flow due to surface sealing of the river, as the most coherent solution to this infiltration problem. Furthermore, a conceptual hidrogeologic model representing the hydrogeological behavior of an open pit mine was created, developing a system of the appropriate use of boundary and constraint conditions, calibrating the model and verifying different flow scenarios, as a result of the incorporation of different water control techniques assessed in transient regime, such as covering pumping wells, cut-off walls as well as wellpoints and horizontal drains. The different techniques modeled showed satisfactory results, with various arrangements of techniques configured in a localized form resulting in the most desirable and efficient treatments for particular problems.