The Albanian part of Lake Ohrid is endangered by heavy metals, the source of which is mainly the old mining waste around the lake shore, but also agricultural pollution. The chromium and nickel concentrations were investigated in the fall season in the sediment and common reed (Phragmites australis). The peroxidation of lipids in stalks was also investigated. The study was conducted on three points of the lake: at the entrance to the city of Pogradec, the former Fe-Ni mine and the village of Lin (control point). Heavy metals were determined with the method of atomic absorption spectrometry and malondialdehyde, using the spectrophotometric method. The results showed that there was greater accumulation of nickel than chromium in both sediments and stalks in the three explored points. The sediment and plant samples taken in the part of the former Fe-Ni mines showed a higher level of investigated metals, compared to the other two research points. At this point, the difference was significant for chromium (p <0.01) compared to the village of Lin, whereas for nickel there was a significant difference (p <0.01) for the two research points compared to the reference point (Lin). Concerning the Cr and Ni levels in stalk, a significant difference (p <0.01) was observed for both metals only in the samples taken from the former Fe-Ni mines, compared to the village of Lin. Meanwhile, the increased MDA level caused by oxidative stress was higher in the plants collected at the entrance of Pogradec, not only with the checkpoint (p <0.01) but also with the plants collected in the former Ni-Fe mine.