There are areas in Africa where malaria occurs and of course you want to protect your child against it. But there are also plenty of areas without malaria, such as much of South Africa, part of Namibia and high-altitude parts of East Africa such as Nairobi. In any case, it is wise to provide long clothes and apply DEET in malaria areas after sunset. Bring your own (impregnated) mosquito net and pre-spray it with DEET. It is also recommended to take Malarone (prophylaxis). Let the GGD or GP advise you well before the trip!
Take care with drinking water. Only give your child water from bottles with the cap still intact (or a plastic wrap around it). If not, or if you’re not sure where the drinking water comes from, err on the side of caution and leave it alone. Also be careful with ice cream and ice cubes, these are often made from tap water.