Carbonate aquifers represent an essential source of water supply worldwide, although they generally have a high intrinsic vulnerability. This results in an elevated risk of groundwater contamination and for human health in case of hazardous anthropic activities such as mining. Hence, for addressing the pollution issues of these strategic groundwater resources, and planning their optimal management as well, detailed surveys based on a comprehensive approach are required. This work concerns the issues tied to the coexistence of abandoned mining activities and valuable groundwater. It provides the case of a past-mining district on the Apuan Alps (northwestern Tuscany, Italy) where the local carbonate aquifers host abundant groundwater resources threatened by acid mine drainages and thallium-contaminated surface waters. The research focuses on three important springs, among which only one is tapped for drinking use. The main goal was to investigate the origin and hydrochemical evolution of groundwater and to evaluate their possible interactions with sources of potentially toxic elements. From September 2017 to December 2018 we performed nine sampling fields on contaminated stream and spring waters, as well as chemical (major and trace elements) and isotopic analysis (δ18O and δ2H), in addition to continuative monitoring of hydrologic-physical–chemical parameters. We also periodically sampled four low-yield springs located in the studied catchment in order to characterize the isotopic signal of the infiltration water and identify the main recharge areas of groundwater systems. We recognize two different groundwater flow systems feeding the main springs. The first one, drained by the two not-tapped springs, is shallower, as evidenced by the over-time evolution of water temperature, electrical conductivity, and isotopic signatures. The Tl concentration and its variability during the study period, which follows the pattern showed by the stream, indicates the likely hydraulic connectivity between the stream and these springs. The second system, feeding the captured spring, is wider and deeper than the former and is characterized by longer residence times. The higher temperature and electrical conductivity, along with the constant O–H isotopic composition, support such a hypothesis. The chemical evolution of the springs starts from a pure Ca-HCO3 end-member, therefore evolving into two different chemical types. On one side, because of the hydraulic connection between the contaminated stream water and the shallower groundwater flow system, significant concentrations SO4, Tl and other potentially toxic elements occur in the not-tapped springs, compromising their quality. On the other hand, the deepening of the flow component drained by the tapped Ca-SO4(HCO3) spring may lead to the dissolution of gypsum/anhydrite layers, thus producing water enriched in SO4 and Sr, although Tl and other potentially toxic elements present very low concentrations. Therefore, the groundwater system feeding this spring appears to be protected from contamination events linked to the Tl-polluted stream water. Moreover, we assessed a very similar recharge average altitude for the two groundwater flow systems, ranging from about 350 m to 450 m a.s.L. In this sector of the catchment, some dismissed mines develop, thus representing a potential source of potentially toxic elements not only through surface acid drainages but also via direct underground transfer. The obtained results highlight the importance of an integrated approach for understanding in detail the groundwater dynamics in complex carbonate aquifers threatened by legacy mining.