The prefecture of Kilkis is a part of the border zone of the north-Greek region and specifically the region of Central Macedonia.On the north it borders with FYROM, on the south with the prefecture of Thessaloniki, on the east with the prefecture of Serres and on the west with the prefecture of Pella.

The natural limits of the prefecture are the basin of Lake Doirani on the north, the Mount Belles (2,031 m.) on the northeast , the mountains Kroussia (860 m.) and Maurovounio on the east, the Mount Paiko on the west and on the south the Mount Vertiskos and the valley of Thessaloniki.The general slope of the area is to the south and particularly to the Thermaikos Gulf.For this reason, most of the rivers, Axios the most important among them, have a similar time.

The prefecture has an area of 2,519 sq. km, which correspond to 13.8% of the total area of the County.65% of its area is flat, well above the respective percentage of the County and much greater than that of the entire country.

The highest mountains of the county are:

• Paiko, with an altitude of 1,650 meters. Its peaks are: the Gola-Tsuka (1,650 m.) Skra (1,097 m.), Pyrgos (1,494 m.), Voulares (1,408 m.), Tsouma (1,219 m.), Vertopia (1490 m.) and Kantasi or Kantasti (1607 m.).
• The mountain Kerkini or Beles. Located in the eastern part of the prefecture, along the borders between Greece, FYROM and Bulgaria. Its highest peak is the Triethnes (1,888 m.). Only a small portion of it belongs to the prefecture of Kilkis.
• The Dysoro or Kroussia. Its highest peak is at 860 m. and the city of Kilkis lies at its foothill.

The Rivers of Kilkis are:

• Axios or Vardaris, which has a length of 83 km and is flowing through the western part of the prefecture. Its riverines are: Mega Rema, emanating from Paiko; Rema Vourkou,   emanating from the heights of   Gynaikokastro; Stravopotamos; Gorgopis etc.
• Gallikos (or Ehedoros), which emanates from Kroussia and flows into Thermaikos Gulf.

The prefecture of Kilkis is plain in its greatest extent. The lowland soils occupy an area of 1,666 sq. km.

Its lakes are: Doirani (or Prassiada) with an area of 33 sq. km, rich in fish, and Pikrolimni with an area ranging from 3.7 to 4.5 sq. km, of which the water has high salinity (three times greater than the Dead Sea) and because of its rocks, has curative and cosmetic properties.

The climate is continental, bolder in the mountains and northern regions of the prefecture.The winter is very cold winter and the summer is warm.