Abstract The physical and chemical effects of bacterial biofilm formation upon hydraulic conductivity, mineral-solution interactions and the formation of biogenic mineral precipitates have been studied over a wide range of scales, from microscopic to macroscopic. Several novel pieces of equipment have been designed, constructed and commissioned in order to measure the physical effects of biofilms upon fluid flow through fractures and porous media, the overall effects of biofilm formation upon mineral surface reactivity, and the imaging and identification of mineral precipitates formed due to the presence of biofilm and bacterial cell surface polymers on a quartz surface. This paper presents an overview of key experimental methods and selected results; further experimental information is being published elsewhere. Biofilm formation with quartz sand in artificial groundwater resulted in a two orders of magnitude reduction in hydraulic conductivity under bench-scale constant head conditions. However, under quasi-environmental conditions within macroscopic centrifuge experiments, a reduction of 21% was measured, revealing differences in measurements and, hence, the value of the macroscopic experimental work in scaling from micro to macro. In-situ microscopic evaluation of biofilms within simulated quartz rock fractures and in porous media reveal only a small percentage of the biomass to be in direct contact with the mineral surface, allowing mineral chemistry to be predominantly controlled by mineral surface reactivity, rather than by a diffusion-limited mineral-biofilm-solution interface. This is true even when a mineral surface is apparently completely covered by biofilm. The alteration of mineral surface drastically increases the kinetics of surface-coordinated trace metal precipitate formation by providing nucleation sites upon extracellular biopolymers and cell wall polymers. Over geological time-scales, these processes, particularly the formation of thermodynamically stable pore-blocking mineral precipitates, are envisaged to markedly change the flow paths, flow rates and interaction of migrating geofluids (water, petroleum, ore-forming solutions) with minerals and rocks.