The water sector of Burundi is faced with the following challenges
- Dilapidated infrastructure as a result of civil war
- Increased water prices especially in urban centers
- Rural water service has insufficient capacities to adequately manage rural water and water supply infrastructures
- Water resources are trans-boundary in nature and shared with her neighbors.
- Inadequate resources in terms of funding, there is limited government funding to water sector
- Limited private sector capacity to cope with demand for water
- Increased pollution of raw water sources especially lakes and rivers.
- Inadequate capacity to plan and implement water sector activities
- Hilly terrain that needs expensive motorized water system has been as one of the challenges to water supply in some areas.