The Atlas of African Lakes compares satellite pictures from decades past with contemporary images.
It plots changes such as the shrinkage of Lake Chad, deforestation around Lake Nakuru in Kenya, and the increasing population around Lake Victoria.
The UN says protecting these lakes is vital if poverty goals are to be met.
"The atlas shows that massive changes are happening in African lakes," said UN Environment Programme (Unep) spokesman Nick Nuttall.
"There are huge population pressures on all lake systems in Africa," he told the BBC News website, "and unless there is some way for people there to find alternative ways of living, they will continue to be under pressure."
Big store
Unep estimates that there are about 677 lakes in Africa, holding a total of 30,000 cubic kilometres of water - the largest stored volume of any continent.
Many are important sources of food and employment.
But natural and human-made problems are combining to reduce the reliability of the water supply, and of foods associated with it.
These include: natural seasonal fluctuations in rainfall climate change pollution over-fishing desertification invasive species innappropriate dam construction
And some important lakes have their own specific issues, such as Lake Songor in Ghana, whose shrinkage Unep attributes to salt production.
"Lakes are the lifeblood of millions and millions of Africans," said Nick Nuttall.
"We are not going to meet the Millennium Development Goals on water or health unless we protect them."
The eight Millennium Goals, agreed by world leaders at the UN in 2000, speak of halving the proportion of people without safe drinking water by 2015, and tackling diseases of children and adults by the same date.
Unep launched its Atlas at the World Lake Conference taking place this week in Nairobi.
A parallel report also compiled for the conference urges African governments to improve multilateral and bilateral agreements on sharing and conserving water.
