Abstract Geochemical mapping based on the analysis of grab samples of organic sediment from more than 40,000 lakes to promote mineral exploration in Newfoundland and Labrador, Canada, was completed in 1987. The usefulness of the resulting regional geochemical data in defining the natural geochemical background for environmental purposes is only now being examined in detail. Questions to be addressed include assessing the magnitude and nature of any widespread contamination of the sediments in relation to naturally occurring levels, how well the data reflect bio-available levels and concentrations in more environmentally critical media such as surface water and soil, and how grab samples of lake sediment reflect anthropogenic chemical change. The stratigraphic variation of trace-elements has been investigated in a relatively undisturbed part of Newfoundland in cores from five lakes selected from the regional geochemical maps to exhibit wide ranges in concentration of several trace elements. Except for extractable Pb, which was enriched up to two-fold in the uppermost 10–20 cm of three cores, the stratigraphic variations of trace-element concentrations in the upper 1–1.5 m of sediment, due to local environmental fluctuations over time, are generally much smaller than geochemical variation between lakes due to the primary geochemical composition of the local bedrock. Preliminary element-speciation studies of the sediments have shown that significant proportions of a wide range of elements (i.e., Cu, Ni, Co, Zn, Y, Dy, La, Cd, Ce, Pb, Mn, V, Fe, Cr, Mo, Ba and Li) are held in acid-leachable organic and amorphous oxide phases of the sediments, indicating their geochemical mobility and potential bio-availability under acid conditions. The geochemical reflection in lake sediment of significant human disturbance of the landscape (urbanization) was studied in the city of St. John's, Newfoundland. Several elements were enriched in the inner-city lakes relative to the local background, most notably Pb which is from 5 to 10 times higher in grab samples of sediment from lakes in the urban core than the upper limit of its natural background for the area. Comparative studies between sediment and water in urban lakes indicate that the spatial distributions of several elements (e.g. Na, Sb, Mg, Pb, K, Cr, Ba, Ti and Sr) are significantly correlated between the two media.