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Lake Prespa, Lake Ohrid and Lake Skadar are the biggest lakes in the Balkan Peninsula. By reason of continuous existence and relatively stable ecological conditions millions years those lakes have a unique collection of flora and fauna. In this paper is presented biodiversity of macrophyte vegetation from Lake Prespa, Lake Ohrid and Lake Skadar. In those three lakes macrophyte vegetation is distributed in zones (belts). The biodiversity of macrophytes is different in those lakes and it is in direct dependence of different altitudes, lakes surfaces and lakes depths.

Submerged macrophytes are useful indicators of nutrient pollution in the littoral of lakes. We analyzed submerged macrophytes at 30 sites in Lake Ohrid (20 in the Macedonian and 10 in the Albanian part). In total, we found 29 macrophyte species, which belong to 9 families. In order to describe and compare nutrient pollution in different parts of Lake Ohrid, and to introduce monitoring methods which are consistent with the demands of the Water Framework Directive we calculated the macrophyte index for each site. The results show that nutrient pollution generally is low in the majority of the investigated sites. There are, however, marked differences among sites, with some sites at the southern part of the lake being more polluted. There also is a marked difference in nutrient pollution between shallow and deeper water. The values of the macrophyte index in deeper waters (> 4 m) indicate that the nutrient pollution is very low, while in shallow waters (< 2 m) it is moderate or moderate-immense.

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