Waters in the vicinity of natural geochemical anomalies such as hydrothermal ore deposits potentially mobilize heavy metals by interaction with primary hydrothermally formed minerals. On the other hand, secondary alteration minerals can retain some of these heavy metals and effectively immobilize them. In order to understand the chemical evolution of waters in such a system, the best way is to compare different waters from various sample locations in a well-defined locality. Thereby one can compare the importance of parameters such as variable flow paths, flow velocities, fluid-host rock interaction and the various sources and sinks of major and trace elements. This was done for the Cu and As deposit of Neubulach in the northern Schwarzwald, Germany. Flowing and dripping waters from three sites in the abandoned mine were sampled monthly over 14 months. The waters were analyzed with respect to their major and trace element concentrations including rare earth elements (REE) to evaluate their seasonal and spatial variation. The three sample types collected from different depths in the mine have different flow paths and are influenced to different extents by the sandstone host rocks, by overlying carbonates and by the hydrothermal barite quartz vein with Cu-Bi-As ores, mainly tennantite, exploited from the former mine. The sample site in the upper part of the mine (“HGS water”) is about 30 m below surface and the amount of water dripping from the roof of the adit is strongly dependent on the precipitation. By contrast, the water collected in the lower part of the mine (about 100 m below surface) is dripping constantly throughout the year and forms abundant calcite sinters (“sinter water”). A third sample was collected monthly from the mine drainage adit (again about 100 m below surface), that collects water from the entire mine (“flowing water”). Elevated Cl and Na concentrations and increased Cl/Br ratios in the HGS waters taken in the winter months during snow melt indicate input of road salt and therefore show the direct influence of surface runoff. By contrast, the sinter water compositions do not show any variation during the year, which suggests that these waters are unaffected by short-time input from the surface; their chemical composition is determined by water-rock interaction only. Rare earth element patterns and Rb/Cs values indicate interaction with clay minerals whereas Cu and As systematics show that tennantite dissolution is incongruent. Although inverse modelling shows that reaction of surface water with the observed phases in the host rocks and in the hydrothermal vein nicely explains the water compositional variations, speciation modeling and calculations of thermodynamic stabilities of various Cu arsenates suggest that secondary alteration minerals may form metastably.