In geo-hazard prone heterogenous mining terrain with multiple geological structures, surface water may interact with its underlying groundwater system conveying large quantities of water to deeper aquifers, which could undoubtedly lead to pit-inflows and slope stability challenges for any close-by mining operation. A total of forty-three (43) water samples were collected from the atmosphere, surface, subsurface and the pit-water during dry and wet seasons, respectively to identify pit-inflow origin using hydrogeochemical evolution paths and end member mixing analysis of the major ions at the only manganese mine in Nsuta, Ghana. The major ions order was Na2+>Ca2+>Mg2+>K+ for cations and anions' order was HCO3− > SO42− > Cl−. The identified hydrogeochemical facies and proportions are Ca–HCO3- (68.75%), Ca–Cl2 (18.75%) and mixed Ca–Mg–Cl (12.5%) in the dry season and mixed Ca–Na–HCO3 (54%) followed by Ca–HCO3 (46%) in the wet season. Na+ is the preeminent cation whilst HCO3− is the preeminent anion. Saturation Index (SI) of carbonate and evaporate minerals, particularly calcite, identified groundwater-surface water (GW-SW) exchange flux pathways in the study area, and thus establishing geochemical modeling as a robust tool for identifying GW-SW exchange flux pathways in riverine and aquifer systems. The isotopic composition of the various water samples is depleted having strong mixing relationship of R2 = 0.96%, suggesting the waters have same origin with low d-excess indicating rainfall under lower humidity. End member mixing analysis suggested GW-SW interaction with the surface water contributing an average of 87% to groundwater in the mine pit during the dry season. The generally low hydrogeochemical and isotopic evidence of the various water sources indicate homogeneity pointing to the existence of GW-SW interaction. The fast-movement of the exchange flux has widened flow path leading to pit slope stability issues and huge pit-inflows. Therefore, the mine managers, stakeholders, and decision makers are strongly advised to promptly integrate hydrogeotechnical assessments into their operations as a sustainable remedial measure. This will enable them to continuously reduce the potentiometric head of the groundwater system and ensure cost-efficient mining activities. It is essential to take these actions due to the mine's location within two river stream catchments.