The rivers of Macedonia mostly belong to the Aegean Basin, with a few emptying into the Adriatic . The river Vardar is the longest river with its 420-kilometre length. Beginning near the village of Vrutok near Gostivar, it empties into the Aegean Sea at Thessaloniki . Its right tributaries are the Treska (138km) and the Crna Reka (222km), as well as the smaller Topolka and Babuna. Its left tributaries are the Lepenec, the Pcinja (127km), and the Bregalnica (184km). Smaller river systems include the 103km-long Strumica River, which flows into the Aegean Sea, and the 122km-long Crn Drim River, which belongs to the Adriatic Basin.

There are three tectonic lakes in Macedonia : Ohrid, Prespa, and Dojran.

Through diluvial glaciations of the mountains of Sar, Jakupica, Bistra, and Baba, a few dozen cirques were formed, some of which were subsequently filled with water and today represent a rare natural beauty. On Mt. Sar alone, there are 14 such "mountain eyes" with a combined surface of 500 square metres, all lying at an altitude of 1,330 to 2,470 metres.

Among the 10 man-made lakes of Macedonia the largest is Lake Tikves, encompassing 14 square kilometres with a depth of 95 metres at an altitude of 260 metres. Slightly smaller is Lake Globocica — covering a surface of 13 square kilometres and 92 metres deep at an altitude of 580 metres. Lake Mavrovo is slightly smaller yet, at 12 square kilometres, 48 metres deep, at an altitude of 1,179 metres.

Mineral waters are a natural treasure of Macedonia, with health resorts built near the thermal-mineral springs at Kosovrasti, Katlanovo, and Kezovica. There are other smaller resorts, as well.