The Water for African Cities Programme aims to reduce the urban water crisis in African cities through efficient and effective water demand management, minimize the environmental impact of urbanization on freshwater resources and boost awareness and information exchange on water management and conservation.  The programme is part of the wider efforts of the agency to meet the Millennium Development Goal targets of halving the number of people without access to safe water and sanitation by 2015, and promoting environmental sustainability.  It also seeks to create an enabling environment for pro-poor investment.

The programme, initiated in December 1999, is a direct follow-up of the Cape Town declaration of 1997 adopted by African ministers to address the urgent need to employ better practices in the management of water resources in African cities. The programme is the first comprehensive initiative to support African countries to effectively manage the growing urban water crisis and protect the continent's threatened water resources and aquatic ecosystems from the increasing volume of land-based pollution from the cities. 

Cities that participated in its first phase include Abidjan (Côte d’Ivoire), Accra (Ghana), Addis Ababa (Ethiopia), Dakar (Senegal), Johannesburg (South Africa) Lusaka (Zambia) and Nairobi (Kenya). The first phase of the programme ended in December 2002.

One of the most notable successes of the first phase of the programme was the wide acceptance of water demand management as the cheapest form of augmenting supply at both utility and national policy-making levels. The implementation of a catchment management strategy also provided a unique platform to bring together diverse stakeholders from the urban water and environment sectors and community groups into action-planning, monitoring and implementation of local environment management of water resources.

During the first phase, a comprehensive strategy for public awareness which focused not only on achieving short term results through public awareness campaigns, but also longer term approaches through water education targeting school children and youth was developed.

The second phase of the Water for African Cities Programme was launched by African Ministers of the African Ministerial Conference on Water (AMCOW) at the Pan African Implementation and Partnership Conference on Water in December 2003.