Colloids, such as submicrometre mineral particles or bacterial cells, can act as carriers enhancing the mobility of poorly soluble contaminants in subsurface environments. Spectroscopic and microscopic analysis of flooded soils suggests that copper colloids and metal sulphide colloids increase the concentration of contaminants in waterlogged soils. Colloids, such as submicrometre mineral particles or bacterial cells, can act as carriers enhancing the mobility of poorly soluble contaminants in subsurface environments1,2. In sulphate-reducing soils and sediments, metal sulphide precipitation has been proposed3,4,5,6 to generate contaminant-bearing sulphide colloids, which could transport contaminants traditionally thought to be immobilized by metal sulphide formation7. However, direct evidence for such a process is lacking. Here, we report the composition and morphology of pore-water colloids formed in contaminated floodplain soil when flooded with synthetic river water over a four-week period. We show that, on flooding, bacteria dispersed in the pore water mobilize copper by inducing biomineralization of metallic copper(0). We suggest that copper(0) crystals form by disproportionation of copper(I), which is released by copper-stressed bacteria to maintain copper homeostasis8,9. Sulphate reduction, which started on the fourth day of flooding, resulted in the mobilization of cadmium and lead, which were partitioned to copper-rich sulphide colloids showing two types of morphology: bacterium-associated ∼50–150-nm-diameter hollow particles formed through copper(0) transformation, and dispersed <50 nm nanoparticles, probably formed through homogeneous precipitation. The slow deposition of both types of sulphide colloid ensured elevated contaminant concentrations in the pore water for weeks. Our findings imply that colloid formation can enhance contaminant release from periodically sulphate-reducing soils and sediments, potentially polluting surface- and groundwaters.