Water supplies from chalk aquifers in northern Europe can be contaminated by semi-metals such as As and metals such as Cr, Ni and many more, as a result of leaks from landfills, industrial sites and from natural oxidation of pyrite in the chalk, releasing trace elements. Chalk, which is predominantly calcite (CaCO3), has the ability to immobilize Ni, but its uptake by chalk is sometimes greater than expected. In an attempt to identify the controls on metal uptake, chalk samples from Klintholm I/S (Fyn, Denmark) were decalcified in EDTA solution and the residue was examined with transmission electron microscopy (TEM) for morphology and composition. Energy dispersive X-ray spectrometry (EDXS) revealed minor Si and Al (probably clay) and major Mn and Fe as (hydr)oxides. These natural nanoparticles have very large surface areas contributing to chalk’s uptake capacity for Ni and other metals from groundwater.