Understanding the resilience of microorganisms to extreme environments and geo-bio interactions contributes to the worldwide challenge posed by abandoned mining wastes. Mining areas are often harsh environments due to extreme pH (low or high pH), toxic metal concentrations, and scarce organic matter. In Sardinia (Italy), Zn-biomineral precipitations along the riverbeds, rhizospheres, and hyporheic zones continuously improve mining-impacted catchment sediment and water quality. Biofilms, characterised by extremophiles, lead to the formation of biominerals (hydrozincite and Zn-silicate) along the riverbed. In wetlands, Phragmites australis and Juncus acutus dominate the rhizosphere, where geomicrobial processes lead to the precipitation of metal-bearing minerals. In the hyporheic zone, reducing conditions within fine sediment layers can enhance the sulphur-reducing bacteria activity, leading to sulphide bioprecipitations. Generally, biominerals show nano-sized crystals agglomerating into different shapes and covering the bacterial extracellular polymeric substances. The metals can occupy a specific position in the biomineral crystal structure and/or be adsorbed by the biomineral or biofilm. Geomicrobial processes occurring at the nano-to mesoscale reduce the metal load in the riverine water, improving the water quality at the catchment scale. Research outputs contribute to the geomicrobial processes knowledge, the implementation of bioremediation technologies, bio-hydrometallurgy, and sustainable biotechnologies. © The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Switzerland AG 2024.