According to www.historymuseum.ca, "In ancient times, the Egyptians called the desert the "red land", distinguishing it from the flood plain around the Nile River, called the "black land". These colors reflect the fact that the desert sands have a reddish hue and the land around the Nile turned black when the annual flood waters receded."
When the Nile River flooded into Upper Egypt during summer and Lower Egypt in the fall, it coated the land surrounding the river in a silt. This silt was great for farming, and made the land a very dark color. This is why it was called the black land.