African Great Lakes and particularly Lake Tanganyika are under pressure of global and local environmental challenges including climatic change and anthropogenic pressures. Important past and present ecological changes were investigated. Possible ways to improve our knowledge of ecological changes are deduced which can be useful to set up a needed long term integrated monitoring. Environmental monitoring has been implemented during various periods in the last decades at Lake Tanganyika. This research project investigates on previous and present monitoring in relation particularly with fisheries, climate, and water quality to identify best adapted strategies for such a wide lake. Various ecological changes have taken place at Lake Tanganyika including lake warming and heavy pressure on various fisheries resources. The implementation of monitoring of several parameters was however often not continuous nor standardized amongst bordering countries. This situation is unfavorable for an optimal ecological investigation of the lake. Long-term monitoring observations are essential to take management measure to adapt to natural changes and decrease whenever possible unfavorable human impact on the great lake environment. There is a real need for regionally standardized long term monitoring including various levels of implementation: a continuous regular monitoring of a key basic variable with additional less frequent or more specific intensive monitoring completing it. The sustainability of continuous regular monitoring requires that it remains focused on a few essential parameters. It needs also to remain inexpensive. Its strength would be its uninterrupted implementation by mandated national authorities with possible support from the international community. Setting up a long term integrated monitoring program is also a goal of the Lake Tanganyika Authority (LTA) and various institutions and scientists. Such long term environmental monitoring needs to be largely encouraged and supported to insure a real sustainability of Lake Tanganyika ecosystems services.