The heavy metal contamination in Lake Ohrid, a lake shared between Albania and Macedonia, was studied. Lake Ohrid is believed to be one of the oldest lakes in the world, with a large variety of endemic species. Different anthropogenic pressures, especially heavy metal influxes from mining activities, might have influenced the fragile equilibrium of the lake ecosystem. Heavy metal concentrations in water, sediment, emergent vegetation, and fish were investigated at selected sites of the lake and a study of the heavy metals in five tributaries was conducted. The lake surface water was found to have low levels of heavy metals, but sediments contained very high levels mostly near river mouths and mineral dump areas with concentrations reaching 1,501 mg/kg for Ni, 576 mg/kg for Cr, 116.8 mg/kg for Co and 64.8 g/kg for Fe. Sequential extraction of metals demonstrates that heavy metals in the sediment are mainly present in the residual fraction varying from 75% to 95% in different sites. High heavy metal levels (400 mg/kg Ni, 89 mg/kg Cr, and 39 mg/kg Co) were found in plants (stem of Phragmites australis), but heavy metals could not be detected in fish tissue (gill, muscle, and liver of Salmo letnica and Salmothymus ohridanus).