The file include the raw data and metadata. The data correspond to the study an earthworm community in an urban wasteland. Over 87 quadrats distributed over all the site we measured the concentrations in 38 elements by X-ray Fluorescence and we sampled the earthworm community in each quadrat. ICP-OES measurements of Cd, Cu, Pb, and Zn concentrations in Lumbricus castaneus individuals and their associated soils were done for 30 of the 87 quadrats in order to study the ability of this species to bioaccumulate metals. Finally, we genotyped 175 individuals of Lumbricus castaneus at 8 microsatellites to study the population genetics of this species at the scale of the site and across the pollution gradient.