The department states that at Platjan water has been covering the nearby bridge since 24 February and travellers are not able to cross the border due to the high levels.
At Zanzibar, the river has been flooded since 16 January and travellers are thus prevented from crossing to reach the port of entry.
Other areas to be affected are Alberton, Randburg and Roodepoort.
Although the water levels at Pontdrift have dropped, travellers are still unable to cross the border.
The department advises travellers using these three ports of entry to use the Groblers Bridge port of entry.
On the Botswana border, the Bray port of entry is also affected by the high levels of the river and travellers are advised to use the Makopong Port of Entry.