The lake forms part of a system of five interconnected low-lying depressions that fill to variable depths depending on the extent of the annual flood of the Niger River.

The more southerly Kondi channel (64 km in length) branches from the Niger a few kilometers downstream of Diré[4] and then meanders across the Killi floodplain.

The larger and more northerly Tassakane channel (104 km in length) branches from the Niger further downstream near Korioumé and then meanders across the Kessou floodplain.

This allows crops to be cultivated around the border of the lake and the growth of Echinochloa stagnina ("bourgou") in low-lying areas to provide dry season pasture.

[14] One of the major aims of a United Nations Sudano-Sahelian Office (UNSO) project (1986-1990) was to improve the connection of the Niger with Lake Faguibine and to cut some of the meanders of the Kondi channel.

During the 1980s the low height of the annual floods created intense competition for water and the local population obstructed the flow in the channels and installed fish-traps.

Since 2003, a German aid organization, Mali-Nord, have financed the construction of irrigated areas that leave the flow of water in the channels unimpeded.

[15] In 2006 the Government of Mali created the "Office pour la Mise en Valeur du système Faguibine" (OMVF) to maintain the channels and to stabilize the sand dunes by planting Euphorbia balsamifera and eucalyptus.

[18] In a project funded by the government of Norway, the United Nations Environment Program is studying the Lake Faquibine ecosystem and looking at ways in which the management of land and the hydrological cycle could be improved.