This paper summarizes international state-of-the-art applications and opportunities for employing and deploying hydrological, geochemical, and isotopic tools in an integrated manner for investigations of mining operations. It is intended to aid formulation of more integrated approaches for evaluating the overall sustainability of mining projects. The focus is particularly on mine waters, including: environmental water sources, mine water dynamics, and as a source and vector for pollution in the wider environment. The guidance is generic to mining projects and not just reflective of a particular extraction (e.g. coal, metalliferous, uranium) industry. A mine life cycle perspective has been adopted to highlight the potential for more integrated investigations at each stage of a mining operation. Three types of mines have been considered: new (i.e. those in the planning stage), active (i.e. working mines), and historical mines (i.e. inactive and abandoned mines). The practical usage of geochemical analyses and isotopic studies described here emphasise characterisation, dynamics, and process understanding for water quality considerations in tandem with water resource and environmental impact implications. Both environmental (i.e. ambient) and applied (i.e. injected) tracers are considered. This guide is written for scientists (including isotope specialists) who have limited or no mine water experience, environmental managers, planners, consultants, and regulators with key interests in planned, active, and legacy mining projects.

Environmental contamination with Mycobacterium tuberculosis complex (MTC) has been considered crucial for bovine tuberculosis persistence in multi-host-pathogen systems. However, MTC contamination has been difficult to detect due to methodological issues. In an attempt to overcome this limitation we developed an improved protocol for the detection of MTC DNA. MTC DNA concentration was estimated by the Most Probable Number (MPN) method. Making use of this protocol we showed that MTC contamination is widespread in different types of environmental samples from the Iberian Peninsula, which supports indirect transmission as a contributing mechanism for the maintenance of bovine tuberculosis in this multi-host-pathogen system. The proportion of MTC DNA positive samples was higher in the bovine tuberculosis-infected than in presumed negative area (0.32 and 0.18, respectively). Detection varied with the type of environmental sample and was more frequent in sediment from dams and less frequent in water also from dams (0.22 and 0.05, respectively). The proportion of MTC-positive samples was significantly higher in spring (p<0.001), but MTC DNA concentration per sample was higher in autumn and lower in summer. The average MTC DNA concentration in positive samples was 0.82 MPN/g (CI₉₅ 0.70–0.98 MPN/g). We were further able to amplify a DNA sequence specific of Mycobacterium bovis/caprae in 4 environmental samples from the bTB-infected area.