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.