Vardar has composite valley because of the sequence of gorges and valleys along its course. The river rises in Vrutok, several kilometres southwest of Gostivar in the northwest part of the Republic of Macedonia. It continues to flow past the town of Gostivar and the valley Polog where several tributaries flow in it: Lakavica, Mazdracha, Pena, Bistrica, Rakita. Then, through the gorge Dervenska Klisura, it enters the Skopje Valley where it accepts water from Lepenec, Treska, Pchinja and the river Markova Reka and it passes through Skopje.

Flowing past the gorge Taorska Klisura where the river Kadina Reka flows into, Vardar, enters the small Veles Valley and it flows past Veles. Here the rivers Topolka and Babuna flow into Vardar. Then, through the gorge Veles Klisura the river enters the Tikvesh valley where two of its biggest tributaries, Crna Reka from the right and Bregalnica from the left side, flow in it. It enters the famous gorge Demirkapiska Klisura, and through it in the Gevgelija-Valandovo Valley ,where it passes the Greek border, it flows past the gorge Ciganska Klisura and flowing past Solunsko Pole it flows into the Aegean Sea west from Thessalonica in Aegean Macedonia.

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The spring of Vardar is rich in fish. There are many bridges along the course of the river, such as the famous bridge Zeleznicki Most in Veles.