The challenges include the following;
- In order for Rwanda to meet its food security needs requires a lot of water for irrigation and for use by the associated companies which is a challenge to the sector.
- The hilly terrain that needs expensive motorized water system has been as one of the challenges to water supply in some areas.
- Rwanda lacks reliable water resources data on quantity and quality that is required for long and medium-term planning.
- Lack of operation and maintenance of the hydro meteorological stations due to financial constraints.
- The impact of lack of hydrological data is that the implementation of the plans to manage the water resources in an equitable and rational manner.
- Poor sanitation, lack of urban and industrial waste water treatment, mining activities and intensive agriculture applying inorganic fertilizers and pesticides seriously pollute surface waters.
- Most towns have outdated water supply infrastructure.
- Rural water service has insufficient capacities to adequately manage rural water.
- The high prices of water.