It is required that you obtain malaria prophylactics before entering Botswana. When purchasing these, please tell your doctor or pharmacist that you intend to visit Botswana. Start your treatment at least 24 hours before entering Botswana and continue taking the pills for 6 weeks after leaving the country. If you suffer from side effects, try taking your malaria prophylactics at night, after dinner as this usually minimises the effect of the symptoms.
Take precautionary measures to prevent contact with mosquitoes, like: sleeping under a bed-net or in a room/tent with mosquito proofing (remember to keep the flaps zipped at all times); spraying your accommodation with insecticide; making use of a mosquito-repelling lotion or stick; and wearing long-sleeve clothing, long trousers and socks when outside at night. Please contact your local doctor before travelling what kind of vaccinations and medications are necessary.

Water in the main towns is usually purified, provided there are no shortages of chlorine, breakdowns, or other mishaps. It's generally fine to drink.

Out in the bush, most of the camps and lodges use water from bore-holes. These underground sources vary in quality, but are normally free from bugs and so perfectly safe to drink. Sometimes it is sweet, at other times the water is a little alkaline or salty. Ask the locals if it is suitable for an unacclimatised visitor to drink, then take their advice.

The water in the Okavango Delta is generally fine to drink. You'll be expected to do so during most budget mokoro trips, which is fine for most backpackers who are in Africa for long trips. There are relatively few people living in the communities in the Delta; contamination levels are very low. However, if you've a sensitive stomach, or are visiting for a short trip, then you'd be best to avoid it and stick to borehole water. (I'd recommend that you do not insist on bottled water as the costs/waste involved in transporting it to you are high, and borehole water is generally fine.)