I am against you and against your river

The word "you" refers to Pharaoh. God speaks to Pharaoh as if Pharaoh were a monster in the river.

I will give the land of Egypt over to desolation and waste

"I will cause Egypt to become a desolate waste"

"your country will become a wasteland". This refers to Pharaoh and represents Egypt, the country he rules over.

"throughout all of Egypt, from Migdol in the north to Syene in the south and the borders of Cush further south"

This is the name of a place in the far northern part of Egypt.

This the name of a town in southern Egypt. It is now called Aswan.

These borders of Cush were south of Syene. Some versions say Sudan or Ethiopia, the modern names of countries south of Egypt.