Cu, Pb, and Hg concentrations were determined in surface sediment samples collected at three sites in San Jorge Bay, northern Chile. This study aims to evaluate differences in their spatial distribution and temporal variability. The highest metal concentrations were found at the site "Puerto", where minerals (Cu and Pb) have been loaded for more than 60 years. On the other hand, Hg does not pose a contamination problem in this bay. Cu and Pb concentrations showed significant variations from 1 year to another. These variations seem to be a consequence of the combination of several factors, including changes in the loading and/or storage of minerals in San Jorge Bay, the dredging of bottom sediments (especially at Puerto), and seasonal changes in physical-chemical properties of the water column that modify the exchange of metals at the sediment-water interface. Differences in the contamination factor and geoaccumulation index suggest that pre-industrial concentrations measured in marine sediments of this geographical zone, were better than geological values (average shale, continental crust average) for evaluating the degree of contamination in this coastal system. Based on these last two indexes, San Jorge Bay has a serious problem of Cu and Pb pollution at the three sampling locations. However, only Cu exceeds the national maximum values used to evaluate ecological risk and the health of marine environments. It is suggested that Chilean environmental legislation for marine sediment quality--presently under technical discussion--is not an efficient tool for protecting the marine ecosystem.