Following defocused ion beam sputtering, large area highly corrugated and faceted nanoripples are formed on calcite (10.4) faces in a self-organized fashion. High resolution AFM imaging reveals that calcite ripples are defined by facets with highly kinked (11.0) and (2-1.12) terminations. In situ AFM imaging during the exposure of such modified calcite surfaces to PbCl2 aqueous solution reveals that the nanostructured calcite surface promotes the uptake of Pb. In addition, we observed the progressive smoothing of the highly reactive calcite facet terminations and the formation of Pb-bearing precipitates elongated in registry with the underlying nanopattern. By SEM-EDS analysis we quantified a remarkable 500% increase of the Pb uptake rate, up to 0.5 atomic weight % per hour, on the nanorippled calcite in comparison to its freshly cleaved (10.4) surfaces. These results suggest that nanostructurated calcite surfaces can be used for developing future systems for lead sequestration from polluted waters.