LTR has been implemented in four phases:

1. Preparation phase (January 1992-June 1993) - during which the following principal activities were carried out: (a) LTR Coordination and International Scientific Committees were established; (b) project's Headquarters was constructed in Bujumbura and research sub-stations in Uvira (DRC), Kigoma (Tanzania) and Mpulungu (Zambia) renovated and equipped; (c) scientific and other equipment was procured and distributed among the research stations; (d) LTR international staff was recruited; (e) national staff was selected and extensively trained; (e) LTR Documentation Centre was established; and, most importantly, (f) the LTR Scientific Sampling Programme (SSP) was designed, field-tested, and approved by both LTR Committees.

2. Operational phase (July 1993-December 1996) - core activities of the LTR Scientific Programme were undertaken through an extensive three-year exercise known as the Scientific Sampling Programme (SSP). This represented a unique approach to the study of the physical and biological processes in the lacustrine ecosystem, in that a standartised methodology was deployed on a regionally integrated and synchronised basis under eight components, namely: (a) hydrodynamic modelling; (b) remote sensing; (c) limnology and primary production; (d) zooplankton biology; (e) fish genetics; (f) fish biology; (g) fish abundance and distribution (fisheries statistics); and (h) assessment of trophic structure and energy flows. Ecosystem assessment of the lake was complemented with other Scientific Programme work that entailed monitoring methods utilising automatic recorders, remote sensing technology, and integrated lake-wide surveys with the project research vessel, the R/V Tanganyika Explorer. A total of 20 lake-wide research cruises in support of hydrodynamic, limnological, fish biological, and hydroacoustic studies were carried out. The R/V Tanganyika Explorer was specially equipped by the project with modern sampling and navigational devices in order to serve as a research platform. Sampling schemes employed on the cruises were designed to accommodate multidisciplinary aims in order to combine physical and ecological observations and facilitate analysis of the interactions between trophic levels.

3. Extension phase (January 1997-December 1998) - evaluation of LTR results during the latter part of 1996 led to recommendations for the continuation of activities as it was recognised that socio-economic and legal-institutional issues needed to be addressed more directly in order to complete the foundation work for a regional framework management plan. As final wrap-up, analysis, and reporting activities for SSP continued, the LTR team embarked on a complementary programme of legal-institutional studies and socio-economic investigations that involved a lake-wide survey of landing sites, fishers, and trader/procesors. Particular efforts were made to collect information on fishery problems and prospects from the viewpoint of local stakeholders.

4. National execution phase (January 1999-December 2001) - organisation and operation under national execution of an extended Lake Tanganyika Fisheries Monitoring Programme is now a primary LTR activity. At the same time, and in collaboration with the interregional FISHCODE Programme, the LTR team has completed the task of synthesising project outcomes and formulated a Framework Fisheries Management Plan (FFMP) for the Tanganyika region. The FFMP was already proposed and approved by the participating States during the CIFA Sub-committee, in Lusaka (May 1999). Efforts are now underway to facilitate FFMP implementation through the preparation of a programme of accompanying measures.