Your first concern in Egypt should be the sun. In this latitude sunburn happens quickly, and the heat itself—shade temperatures are very often in the upper 90s (Fahrenheit)—is intense. In the dry desert areas, you might not feel that you're sweating, when in fact your body is losing considerable amounts of water.
Take extreme care to protect yourself from the sun by covering your skin and using high-level sunblocks. Always carry bottled water and keep up your water intake. Dehydration can be a serious problem, so replenish your fluid levels regularly.
In Egypt the major health risk is "gippy tummy"—traveler's diarrhea varying in intensity from mild to disablingly severe. It's almost certainly attributable to contaminated water, and, consequently, you are strongly advised to drink only bottled water (or water that has been boiled for at least several minutes), avoid uncooked vegetables with a high water content (lettuce, green salads, watermelon), and be very wary of taking ice in drinks. When eating out, ask for your drinks min gheir talg (without ice), and always request mayya ma'daniya (bottled water). Check to make sure that the seal on your bottled water is intact before drinking it. However, precautions are often of no avail. A cruise of some 90 British medical doctors and their spouses found 70 members out of action for three days. People who consumed identical meals at the same table were hit randomly. Staying at the very best international hotels won't necessarily protect you from this.
Mild cases may respond to Imodium (known generically as loperamide) or Pepto-Bismol (not as strong), both of which can be purchased over the counter; paregoric, another antidiarrheal agent, requires a doctor's prescription in Egypt.
Drink plenty of purified water or tea—chamomile (babunag) is a good folk remedy. In severe cases, rehydrate yourself with a salt-sugar solution (½ teaspoon salt and 4 tablespoons sugar per quart of water).
According to the U.S. government's National Centers for Disease Control and Prevention (CDC), there's a limited risk in Egypt of malaria and dengue fever, diseases carried by insects, and some risk of schistosomiasis, a parasitic infection acquired by swimming in fresh water. Malaria poses almost no risk to travelers visiting major tourist areas in North Africa. One exception is al-Fayyum oasis.
Swimming in the Nile, or in fresh water anywhere in Egypt, is highly discouraged and should be reserved for well-chlorinated pools or salt water. Prepare yourself for the most common illness that befalls travelers by bringing antidiarrheal tablets with you from home. Also as a preventative, adults and children should complete Hepatitis A and B and tetanus shots at least a month before traveling.