The chemical and isotopic compositions of river and groundwater reflect the different natural processes that provide chemical elements to the dissolved load, i.e. mainly the weathering of rocks and soils, atmospheric inputs and anthropogenic disturbances. This study reports on the geochemistry of surface- and groundwater along a part of the Subarnarekha River system (north-eastern India) collected during monsoon and dry season, during a monitoring program aimed at evaluating impacts of mining and metallurgy on the river system. The aquifer is of fracture type and the seasonal behaviour, groundwater flow conditions and pollutant transfer were observed through a network of 69 wells with typical depths of 50 meters. Geochemical observations, including major cations and anions, trace element concentrations and isotopic tracing (stable isotopes of the water molecule, strontium isotopes) come to conclusions on the origin and the relationships between the surface- and groundwater in the studied catchment. A large range of salinities is observed in surface- and groundwater, both for dry or wet periods. Surface water samples plot within the field HCO3-Ca during both water stages. Most groundwater samples plot within the field of Ca-SO4 water type and HCO3-Ca water type. This reflects the high Ca input in groundwater, other than weathering. Such inputs could be related to (i) carbonate amendments used in agricultural practices and (ii) residues from ore processing. With regards to stable isotopes 18O and 2H, many groundwater samples plot between local meteoric water lines and the global meteoric water line, reflecting a meteoric origin for the water without any major transformation like evaporation. This suggests that transfer from rainfall towards groundwater storage through soils and the non-saturated zone is fast. The scatter of 87Sr/86Sr signatures in surface- and groundwater cannot be explained by less than 3 end-member compositions. The most dilute end-member should be compatible with rainwater inputs. The most mineralised end-member has isotopic compositions very similar to the dilute one, and is believed to represent anthropogenic inputs. The third end-member is characterised by an intermediate Sr content and a more radiogenic signature. It is believed to be controlled by a natural background, however affected by human activities (e.g. drainage of mine waste). Potential flow paths were investigated north of the area. Under the light of different geochemical tools, all groundwater types in this area seem to evolve more as in close pockets than along a flow path. This is consistent with groundwater head contour maps that do not reflect any groundwater flow directions, as groundwater bodies evolve in discontinuous or isolated units. The limited extent of transfer and the predominance of natural phenomena contribute to explain the moderate level of groundwater contamination and the characteristics of surface water contamination by mining and metallurgy.