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Five major drainage basins exist in the country:
- The Limpopo basin occupies about 14 percent of the country in the east;
- The Orange basin occupies about 12 percent in the south;
- The Zambezi basin occupies a small area (2 percent) in the north;
- The Okavango basin, which is an endorheic basin, occupies about 9 percent in the northwest;
- The South Interior, which also is an endorheic basin, occupies the remaining area (about 63 percent) and includes the Kalahari Desert and the Makgadikgadi Pans.
Low rates of surface runoff and groundwater recharge are typical. Even during the wet season stream flow is not continuous, with internal rivers only flowing for 10-75 days a year. The Okavango Delta in the northwest is a large inland delta including about 6 000 km2 of permanent swamp and between 7 000 and 12 000 km2 of seasonally inundated swampland. Together with the Chobe and Linyati rivers, it accounts for 95 percent of all surface water in the country. An estimated 11 km3 of water flows every year into the delta, but most of it is lost through evapotranspiration. There is a spillway from this area to the Chobe river in the Zambezi basin in periods of high floods.
Internal renewable surface water resources are estimated at 0.8 km3/year. Most dams on rivers have been constructed for urban water supplies or for livestock watering. The major dams are constructed on the larger rivers and some have required international agreements. It is considered that most ‘good’ sites for larger dams have now been used or are reserved for large water supply dams (for urban and industrial water uses), which are expected to be constructed in the near future. The smaller dams on smaller rivers currently suffer from sedimentation and irregular stream flows, making planning for use by irrigation difficult. Many earth dams built for livestock watering and irrigation (over 240 since 1970) have also suffered from lack of maintenance and many are now not in use.
Groundwater resources are used throughout the country for livestock and municipal watering and for small areas of irrigation. These resources are geologically old and quality can be affected by salinity and concentrations of fluorides, nitrates and other elements. Current groundwater recharge rates are equivalent to about 1.7 km3/year. Considering an overlap of about 0.1 km3/year between surface water and groundwater, the total internal renewable water resources are 2.4 km3/year (Table 2). In most parts of Botswana groundwater abstraction effectively mines a limited resource. It is estimated that over 21 000 boreholes exist in the country, but many are not used and capped. Just over half of the registered boreholes in the country are owned by the government, the remainder by private individuals. Although the amount of water potentially available is large, it is relatively expensive to exploit and it is saline in many places. Aquifers also have to be protected carefully from contamination, mainly caused by faecal material from septic tanks and pit latrines.