A borehole drilling campaign has allowed the study of a former littoral lagoon located next to the harbour city of Cartagena in South-East Spain (close to the Sierra de Cartagena polymetallic ore deposits). This lagoon, which developed during the Holocene, was first a shallow sedimentary marine environment and later evolved into a swampy semi-endorheic basin named "Almarjal" (after the Arab term from the fourteenth century). The lagoon eventually dried out and at present forms part of the substratum of the modern sector of the city urban area. The basin representative sediments are sapropelic black silty facies forming a continuous sedimentary archive, accounting for more than 8000 years of depositional phenomena. The geochemical study of these sediments, together with their absolute calibrated dating by C, allows definition of successive stages of mining and metallurgical activities in the area. In turn, this information provides a more comprehensive perspective regarding metal pollution, particularly lead contamination during different periods of the Recent Prehistory and the Classical Age. The results indicate that the beginning of contamination by lead and other heavy metals occurred as early as 4500 years ago, when the Final Chalcolithic period was taking place in the South-East of the Iberian Peninsula. This finding provides further insights regarding the debate on the origins of lead mining and metallurgy in SE Spain.